Daily Papers

Graphs are essential data structures for modeling complex interactions in domains such as social networks, molecular structures, and biological systems. Graph-level tasks, which predict properties or classes for the entire graph, are critical for applications, such as molecular property prediction and subgraph counting. Graph Neural Networks (GNNs) have shown promise in these tasks, but their evaluations are often limited to narrow datasets, tasks, and inconsistent experimental setups, restricting their generalizability. To address these limitations, we propose a unified evaluation framework for graph-level GNNs. This framework provides a standardized setting to evaluate GNNs across diverse datasets, various graph tasks (e.g., graph classification and regression), and challenging scenarios, including noisy, imbalanced, and few-shot graphs. Additionally, we propose a novel GNN model with enhanced expressivity and generalization capabilities. Specifically, we enhance the expressivity of GNNs through a k-path rooted subgraph approach, enabling the model to effectively count subgraphs (e.g., paths and cycles). Moreover, we introduce a unified graph contrastive learning algorithm for graphs across diverse domains, which adaptively removes unimportant edges to augment graphs, thereby significantly improving generalization performance. Extensive experiments demonstrate that our model achieves superior performance against fourteen effective baselines across twenty-seven graph datasets, establishing it as a robust and generalizable model for graph-level tasks.

Graph-level anomaly detection has gained significant attention as it finds applications in various domains, such as cancer diagnosis and enzyme prediction. However, existing methods fail to capture the spectral properties of graph anomalies, resulting in unexplainable framework design and unsatisfying performance. In this paper, we re-investigate the spectral differences between anomalous and normal graphs. Our main observation shows a significant disparity in the accumulated spectral energy between these two classes. Moreover, we prove that the accumulated spectral energy of the graph signal can be represented by its Rayleigh Quotient, indicating that the Rayleigh Quotient is a driving factor behind the anomalous properties of graphs. Motivated by this, we propose Rayleigh Quotient Graph Neural Network (RQGNN), the first spectral GNN that explores the inherent spectral features of anomalous graphs for graph-level anomaly detection. Specifically, we introduce a novel framework with two components: the Rayleigh Quotient learning component (RQL) and Chebyshev Wavelet GNN with RQ-pooling (CWGNN-RQ). RQL explicitly captures the Rayleigh Quotient of graphs and CWGNN-RQ implicitly explores the spectral space of graphs. Extensive experiments on 10 real-world datasets show that RQGNN outperforms the best rival by 6.74% in Macro-F1 score and 1.44% in AUC, demonstrating the effectiveness of our framework. Our code is available at https://github.com/xydong127/RQGNN.

Graph-level anomaly detection aims to identify anomalous graphs from a collection of graphs in an unsupervised manner. A common assumption of anomaly detection is that a reasonable decision boundary has a hypersphere shape, but may appear some non-conforming phenomena in high dimensions. Towards this end, we firstly propose a novel deep graph-level anomaly detection model, which learns the graph representation with maximum mutual information between substructure and global structure features while exploring a hypersphere anomaly decision boundary. The idea is to ensure the training data distribution consistent with the decision hypersphere via an orthogonal projection layer. Moreover, we further perform the bi-hypersphere compression to emphasize the discrimination of anomalous graphs from normal graphs. Note that our method is not confined to graph data and is applicable to anomaly detection of other data such as images. The numerical and visualization results on benchmark datasets demonstrate the effectiveness and superiority of our methods in comparison to many baselines and state-of-the-arts.

Graph representation learning is a fundamental research theme and can be generalized to benefit multiple downstream tasks from the node and link levels to the higher graph level. In practice, it is desirable to develop task-agnostic general graph representation learning methods that are typically trained in an unsupervised manner. Related research reveals that the power of graph representation learning methods depends on whether they can differentiate distinct graph structures as different embeddings and map isomorphic graphs to consistent embeddings (i.e., the isomorphic consistency of graph models). However, for task-agnostic general graph representation learning, existing unsupervised graph models, represented by the variational graph auto-encoders (VGAEs), can only keep the isomorphic consistency within the subgraphs of 1-hop neighborhoods and thus usually manifest inferior performance on the more difficult higher-level tasks. To overcome the limitations of existing unsupervised methods, in this paper, we propose the Isomorphic-Consistent VGAE (IsoC-VGAE) for multi-level task-agnostic graph representation learning. We first devise a decoding scheme to provide a theoretical guarantee of keeping the isomorphic consistency under the settings of unsupervised learning. We then propose the Inverse Graph Neural Network (Inv-GNN) decoder as its intuitive realization, which trains the model via reconstructing the GNN node embeddings with multi-hop neighborhood information, so as to maintain the high-order isomorphic consistency within the VGAE framework. We conduct extensive experiments on the representative graph learning tasks at different levels, including node classification, link prediction and graph classification, and the results verify that our proposed model generally outperforms both the state-of-the-art unsupervised methods and representative supervised methods.

Contrastive learning is an effective unsupervised method in graph representation learning, and the key component of contrastive learning lies in the construction of positive and negative samples. Previous methods usually utilize the proximity of nodes in the graph as the principle. Recently, the data-augmentation-based contrastive learning method has advanced to show great power in the visual domain, and some works extended this method from images to graphs. However, unlike the data augmentation on images, the data augmentation on graphs is far less intuitive and much harder to provide high-quality contrastive samples, which leaves much space for improvement. In this work, by introducing an adversarial graph view for data augmentation, we propose a simple but effective method, Adversarial Graph Contrastive Learning (ARIEL), to extract informative contrastive samples within reasonable constraints. We develop a new technique called information regularization for stable training and use subgraph sampling for scalability. We generalize our method from node-level contrastive learning to the graph level by treating each graph instance as a super-node. ARIEL consistently outperforms the current graph contrastive learning methods for both node-level and graph-level classification tasks on real-world datasets. We further demonstrate that ARIEL is more robust in the face of adversarial attacks.

Recent years have witnessed the great success of graph pre-training for graph representation learning. With hundreds of graph pre-training tasks proposed, integrating knowledge acquired from multiple pre-training tasks has become a popular research topic. In this paper, we identify two important collaborative processes for this topic: (1) select: how to select an optimal task combination from a given task pool based on their compatibility, and (2) weigh: how to weigh the selected tasks based on their importance. While there currently has been a lot of work focused on weighing, comparatively little effort has been devoted to selecting. This paper proposes a novel instance-level framework for integrating multiple graph pre-training tasks, Weigh And Select (WAS), where the two collaborative processes, weighing and selecting, are combined by decoupled siamese networks. Specifically, it first adaptively learns an optimal combination of tasks for each instance from a given task pool, based on which a customized instance-level task weighing strategy is learned. Extensive experiments on 16 graph datasets across node-level and graph-level downstream tasks have demonstrated that by combining a few simple but classical tasks, WAS can achieve comparable performance to other leading counterparts. The code is available at https://github.com/TianyuFan0504/WAS.

Self-supervised learning of graph neural networks (GNNs) aims to learn an accurate representation of the graphs in an unsupervised manner, to obtain transferable representations of them for diverse downstream tasks. Predictive learning and contrastive learning are the two most prevalent approaches for graph self-supervised learning. However, they have their own drawbacks. While the predictive learning methods can learn the contextual relationships between neighboring nodes and edges, they cannot learn global graph-level similarities. Contrastive learning, while it can learn global graph-level similarities, its objective to maximize the similarity between two differently perturbed graphs may result in representations that cannot discriminate two similar graphs with different properties. To tackle such limitations, we propose a framework that aims to learn the exact discrepancy between the original and the perturbed graphs, coined as Discrepancy-based Self-supervised LeArning (D-SLA). Specifically, we create multiple perturbations of the given graph with varying degrees of similarity, and train the model to predict whether each graph is the original graph or the perturbed one. Moreover, we further aim to accurately capture the amount of discrepancy for each perturbed graph using the graph edit distance. We validate our D-SLA on various graph-related downstream tasks, including molecular property prediction, protein function prediction, and link prediction tasks, on which ours largely outperforms relevant baselines.

Graph Neural Networks (GNNs) have become increasingly important due to their representational power and state-of-the-art predictive performance on many fundamental learning tasks. Despite this success, GNNs suffer from fairness issues that arise as a result of the underlying graph data and the fundamental aggregation mechanism that lies at the heart of the large class of GNN models. In this article, we examine and categorize fairness techniques for improving the fairness of GNNs. Previous work on fair GNN models and techniques are discussed in terms of whether they focus on improving fairness during a preprocessing step, during training, or in a post-processing phase. Furthermore, we discuss how such techniques can be used together whenever appropriate, and highlight the advantages and intuition as well. We also introduce an intuitive taxonomy for fairness evaluation metrics including graph-level fairness, neighborhood-level fairness, embedding-level fairness, and prediction-level fairness metrics. In addition, graph datasets that are useful for benchmarking the fairness of GNN models are summarized succinctly. Finally, we highlight key open problems and challenges that remain to be addressed.

This work introduces DiGress, a discrete denoising diffusion model for generating graphs with categorical node and edge attributes. Our model utilizes a discrete diffusion process that progressively edits graphs with noise, through the process of adding or removing edges and changing the categories. A graph transformer network is trained to revert this process, simplifying the problem of distribution learning over graphs into a sequence of node and edge classification tasks. We further improve sample quality by introducing a Markovian noise model that preserves the marginal distribution of node and edge types during diffusion, and by incorporating auxiliary graph-theoretic features. A procedure for conditioning the generation on graph-level features is also proposed. DiGress achieves state-of-the-art performance on molecular and non-molecular datasets, with up to 3x validity improvement on a planar graph dataset. It is also the first model to scale to the large GuacaMol dataset containing 1.3M drug-like molecules without the use of molecule-specific representations.

Artificial General Intelligence (AGI) has revolutionized numerous fields, yet its integration with graph data, a cornerstone in our interconnected world, remains nascent. This paper presents a pioneering survey on the emerging domain of graph prompts in AGI, addressing key challenges and opportunities in harnessing graph data for AGI applications. Despite substantial advancements in AGI across natural language processing and computer vision, the application to graph data is relatively underexplored. This survey critically evaluates the current landscape of AGI in handling graph data, highlighting the distinct challenges in cross-modality, cross-domain, and cross-task applications specific to graphs. Our work is the first to propose a unified framework for understanding graph prompt learning, offering clarity on prompt tokens, token structures, and insertion patterns in the graph domain. We delve into the intrinsic properties of graph prompts, exploring their flexibility, expressiveness, and interplay with existing graph models. A comprehensive taxonomy categorizes over 100 works in this field, aligning them with pre-training tasks across node-level, edge-level, and graph-level objectives. Additionally, we present, ProG, a Python library, and an accompanying website, to support and advance research in graph prompting. The survey culminates in a discussion of current challenges and future directions, offering a roadmap for research in graph prompting within AGI. Through this comprehensive analysis, we aim to catalyze further exploration and practical applications of AGI in graph data, underlining its potential to reshape AGI fields and beyond. ProG and the website can be accessed by https://github.com/WxxShirley/Awesome-Graph-Prompt, and https://github.com/sheldonresearch/ProG, respectively.

Graph Structure Learning (GSL) has recently garnered considerable attention due to its ability to optimize both the parameters of Graph Neural Networks (GNNs) and the computation graph structure simultaneously. Despite the proliferation of GSL methods developed in recent years, there is no standard experimental setting or fair comparison for performance evaluation, which creates a great obstacle to understanding the progress in this field. To fill this gap, we systematically analyze the performance of GSL in different scenarios and develop a comprehensive Graph Structure Learning Benchmark (GSLB) curated from 20 diverse graph datasets and 16 distinct GSL algorithms. Specifically, GSLB systematically investigates the characteristics of GSL in terms of three dimensions: effectiveness, robustness, and complexity. We comprehensively evaluate state-of-the-art GSL algorithms in node- and graph-level tasks, and analyze their performance in robust learning and model complexity. Further, to facilitate reproducible research, we have developed an easy-to-use library for training, evaluating, and visualizing different GSL methods. Empirical results of our extensive experiments demonstrate the ability of GSL and reveal its potential benefits on various downstream tasks, offering insights and opportunities for future research. The code of GSLB is available at: https://github.com/GSL-Benchmark/GSLB.

Devising augmentations for graph contrastive learning is challenging due to their irregular structure, drastic distribution shifts, and nonequivalent feature spaces across datasets. We introduce LG2AR, Learning Graph Augmentations to Learn Graph Representations, which is an end-to-end automatic graph augmentation framework that helps encoders learn generalizable representations on both node and graph levels. LG2AR consists of a probabilistic policy that learns a distribution over augmentations and a set of probabilistic augmentation heads that learn distributions over augmentation parameters. We show that LG2AR achieves state-of-the-art results on 18 out of 20 graph-level and node-level benchmarks compared to previous unsupervised models under both linear and semi-supervised evaluation protocols. The source code will be released here: https://github.com/kavehhassani/lg2ar

Rationale discovery is defined as finding a subset of the input data that maximally supports the prediction of downstream tasks. In graph machine learning context, graph rationale is defined to locate the critical subgraph in the given graph topology, which fundamentally determines the prediction results. In contrast to the rationale subgraph, the remaining subgraph is named the environment subgraph. Graph rationalization can enhance the model performance as the mapping between the graph rationale and prediction label is viewed as invariant, by assumption. To ensure the discriminative power of the extracted rationale subgraphs, a key technique named "intervention" is applied. The core idea of intervention is that given any changing environment subgraphs, the semantics from the rationale subgraph is invariant, which guarantees the correct prediction result. However, most, if not all, of the existing rationalization works on graph data develop their intervention strategies on the graph level, which is coarse-grained. In this paper, we propose well-tailored intervention strategies on graph data. Our idea is driven by the development of Transformer models, whose self-attention module provides rich interactions between input nodes. Based on the self-attention module, our proposed invariant graph Transformer (IGT) can achieve fine-grained, more specifically, node-level and virtual node-level intervention. Our comprehensive experiments involve 7 real-world datasets, and the proposed IGT shows significant performance advantages compared to 13 baseline methods.

In this paper, we propose the first framework that enables solving graph learning tasks of all levels (node, edge and graph) and all types (generation, regression and classification) with one model. We first propose Latent Graph Diffusion (LGD), a generative model that can generate node, edge, and graph-level features of all categories simultaneously. We achieve this goal by embedding the graph structures and features into a latent space leveraging a powerful encoder which can also be decoded, then training a diffusion model in the latent space. LGD is also capable of conditional generation through a specifically designed cross-attention mechanism. Then we formulate prediction tasks including regression and classification as (conditional) generation, which enables our LGD to solve tasks of all levels and all types with provable guarantees. We verify the effectiveness of our framework with extensive experiments, where our models achieve state-of-the-art or highly competitive results across generation and regression tasks.

Graph Neural Networks (GNNs) have demonstrated superior performance on various graph learning tasks, including recommendation, where they leverage user-item collaborative filtering signals in graphs. However, theoretical formulations of their capability are scarce, despite their empirical effectiveness in state-of-the-art recommender models. Recently, research has explored the expressiveness of GNNs in general, demonstrating that message passing GNNs are at most as powerful as the Weisfeiler-Lehman test, and that GNNs combined with random node initialization are universal. Nevertheless, the concept of "expressiveness" for GNNs remains vaguely defined. Most existing works adopt the graph isomorphism test as the metric of expressiveness, but this graph-level task may not effectively assess a model's ability in recommendation, where the objective is to distinguish nodes of different closeness. In this paper, we provide a comprehensive theoretical analysis of the expressiveness of GNNs in recommendation, considering three levels of expressiveness metrics: graph isomorphism (graph-level), node automorphism (node-level), and topological closeness (link-level). We propose the topological closeness metric to evaluate GNNs' ability to capture the structural distance between nodes, which aligns closely with the objective of recommendation. To validate the effectiveness of this new metric in evaluating recommendation performance, we introduce a learning-less GNN algorithm that is optimal on the new metric and can be optimal on the node-level metric with suitable modification. We conduct extensive experiments comparing the proposed algorithm against various types of state-of-the-art GNN models to explore the explainability of the new metric in the recommendation task. For reproducibility, implementation codes are available at https://github.com/HKUDS/GTE.

Graph neural networks (GNNs) are one of the most popular approaches to using deep learning on graph-structured data, and they have shown state-of-the-art performances on a variety of tasks. However, according to a recent study, a careful choice of pooling functions, which are used for the aggregation and readout operations in GNNs, is crucial for enabling GNNs to extrapolate. Without proper choices of pooling functions, which varies across tasks, GNNs completely fail to generalize to out-of-distribution data, while the number of possible choices grows exponentially with the number of layers. In this paper, we present GNP, a L^p norm-like pooling function that is trainable end-to-end for any given task. Notably, GNP generalizes most of the widely-used pooling functions. We verify experimentally that simply using GNP for every aggregation and readout operation enables GNNs to extrapolate well on many node-level, graph-level, and set-related tasks; and GNP sometimes performs even better than the best-performing choices among existing pooling functions.

Vision-language navigation (VLN), which entails an agent to navigate 3D environments following human instructions, has shown great advances. However, current agents are built upon panoramic observations, which hinders their ability to perceive 3D scene geometry and easily leads to ambiguous selection of panoramic view. To address these limitations, we present a BEV Scene Graph (BSG), which leverages multi-step BEV representations to encode scene layouts and geometric cues of indoor environment under the supervision of 3D detection. During navigation, BSG builds a local BEV representation at each step and maintains a BEV-based global scene map, which stores and organizes all the online collected local BEV representations according to their topological relations. Based on BSG, the agent predicts a local BEV grid-level decision score and a global graph-level decision score, combined with a sub-view selection score on panoramic views, for more accurate action prediction. Our approach significantly outperforms state-of-the-art methods on REVERIE, R2R, and R4R, showing the potential of BEV perception in VLN.

The Transformer architecture has become a dominant choice in many domains, such as natural language processing and computer vision. Yet, it has not achieved competitive performance on popular leaderboards of graph-level prediction compared to mainstream GNN variants. Therefore, it remains a mystery how Transformers could perform well for graph representation learning. In this paper, we solve this mystery by presenting Graphormer, which is built upon the standard Transformer architecture, and could attain excellent results on a broad range of graph representation learning tasks, especially on the recent OGB Large-Scale Challenge. Our key insight to utilizing Transformer in the graph is the necessity of effectively encoding the structural information of a graph into the model. To this end, we propose several simple yet effective structural encoding methods to help Graphormer better model graph-structured data. Besides, we mathematically characterize the expressive power of Graphormer and exhibit that with our ways of encoding the structural information of graphs, many popular GNN variants could be covered as the special cases of Graphormer.

Vulnerability identification is crucial to protect the software systems from attacks for cyber security. It is especially important to localize the vulnerable functions among the source code to facilitate the fix. However, it is a challenging and tedious process, and also requires specialized security expertise. Inspired by the work on manually-defined patterns of vulnerabilities from various code representation graphs and the recent advance on graph neural networks, we propose Devign, a general graph neural network based model for graph-level classification through learning on a rich set of code semantic representations. It includes a novel Conv module to efficiently extract useful features in the learned rich node representations for graph-level classification. The model is trained over manually labeled datasets built on 4 diversified large-scale open-source C projects that incorporate high complexity and variety of real source code instead of synthesis code used in previous works. The results of the extensive evaluation on the datasets demonstrate that Devign outperforms the state of the arts significantly with an average of 10.51% higher accuracy and 8.68\% F1 score, increases averagely 4.66% accuracy and 6.37% F1 by the Conv module.

While most network embedding techniques model the relative positions of nodes in a network, recently there has been significant interest in structural embeddings that model node role equivalences, irrespective of their distances to any specific nodes. We present PhUSION, a proximity-based unified framework for computing structural and positional node embeddings, which leverages well-established methods for calculating node proximity scores. Clarifying a point of contention in the literature, we show which step of PhUSION produces the different kinds of embeddings and what steps can be used by both. Moreover, by aggregating the PhUSION node embeddings, we obtain graph-level features that model information lost by previous graph feature learning and kernel methods. In a comprehensive empirical study with over 10 datasets, 4 tasks, and 35 methods, we systematically reveal successful design choices for node and graph-level machine learning with embeddings.

We introduce a self-supervised approach for learning node and graph level representations by contrasting structural views of graphs. We show that unlike visual representation learning, increasing the number of views to more than two or contrasting multi-scale encodings do not improve performance, and the best performance is achieved by contrasting encodings from first-order neighbors and a graph diffusion. We achieve new state-of-the-art results in self-supervised learning on 8 out of 8 node and graph classification benchmarks under the linear evaluation protocol. For example, on Cora (node) and Reddit-Binary (graph) classification benchmarks, we achieve 86.8% and 84.5% accuracy, which are 5.5% and 2.4% relative improvements over previous state-of-the-art. When compared to supervised baselines, our approach outperforms them in 4 out of 8 benchmarks. Source code is released at: https://github.com/kavehhassani/mvgrl

Graph Neural Networks (GNNs) have been widely adopted for drug discovery with molecular graphs. Nevertheless, current GNNs are mainly good at leveraging short-range interactions (SRI) but struggle to capture long-range interactions (LRI), both of which are crucial for determining molecular properties. To tackle this issue, we propose a method that implicitly projects all original atoms into a few Neural Atoms, which abstracts the collective information of atomic groups within a molecule. Specifically, we explicitly exchange the information among neural atoms and project them back to the atoms' representations as an enhancement. With this mechanism, neural atoms establish the communication channels among distant nodes, effectively reducing the interaction scope of arbitrary node pairs into a single hop. To provide an inspection of our method from a physical perspective, we reveal its connection with the traditional LRI calculation method, Ewald Summation. We conduct extensive experiments on three long-range graph benchmarks, covering both graph-level and link-level tasks on molecular graphs. We empirically justify that our method can be equipped with an arbitrary GNN and help to capture LRI.

There is an increasing need to bring machine learning to a wide diversity of hardware devices. Current frameworks rely on vendor-specific operator libraries and optimize for a narrow range of server-class GPUs. Deploying workloads to new platforms -- such as mobile phones, embedded devices, and accelerators (e.g., FPGAs, ASICs) -- requires significant manual effort. We propose TVM, a compiler that exposes graph-level and operator-level optimizations to provide performance portability to deep learning workloads across diverse hardware back-ends. TVM solves optimization challenges specific to deep learning, such as high-level operator fusion, mapping to arbitrary hardware primitives, and memory latency hiding. It also automates optimization of low-level programs to hardware characteristics by employing a novel, learning-based cost modeling method for rapid exploration of code optimizations. Experimental results show that TVM delivers performance across hardware back-ends that are competitive with state-of-the-art, hand-tuned libraries for low-power CPU, mobile GPU, and server-class GPUs. We also demonstrate TVM's ability to target new accelerator back-ends, such as the FPGA-based generic deep learning accelerator. The system is open sourced and in production use inside several major companies.

The Neural Architecture Search (NAS) problem is typically formulated as a graph search problem where the goal is to learn the optimal operations over edges in order to maximise a graph-level global objective. Due to the large architecture parameter space, efficiency is a key bottleneck preventing NAS from its practical use. In this paper, we address the issue by framing NAS as a multi-agent problem where agents control a subset of the network and coordinate to reach optimal architectures. We provide two distinct lightweight implementations, with reduced memory requirements (1/8th of state-of-the-art), and performances above those of much more computationally expensive methods. Theoretically, we demonstrate vanishing regrets of the form O(sqrt(T)), with T being the total number of rounds. Finally, aware that random search is an, often ignored, effective baseline we perform additional experiments on 3 alternative datasets and 2 network configurations, and achieve favourable results in comparison.

During early optimization passes, compilers must make predictions for machine-dependent characteristics such as execution unit utilization, number of register spills, latency, throughput etc. to generate better code. Often a hand-written static/analytical hardware cost model is built into the compiler. However, the need for more sophisticated and varied predictions has become more pronounced with the development of deep learning compilers which need to optimize dataflow graphs. Such compilers usually employ a much higher level MLIR form as an IR representation before lowering to traditional LLVM-IR. A static/analytical cost model in such a scenario is cumbersome and error prone as the opcodes represent very high level algebraic/arithmetic operations. Hence, we develop a machine learning-based cost model for high-level MLIR which can predict different target variables of interest such as CPU/GPU/xPU utilization, instructions executed, register usage etc. By considering the incoming MLIR as a text input a la NLP models we can apply well-known techniques from modern NLP research to help predict hardware characteristics more accurately. We expect such precise ML-driven hardware cost models to guide our deep learning compiler in graph level optimizations around operator fusion, local memory allocation, kernel scheduling etc. as well as in many kernel-level optimizations such as loop interchange, LICM and unroll. We report early work-in -progress results of developing such models on high-level MLIR representing dataflow graphs emitted by Pytorch/Tensorflow-like frameworks as well as lower-level dialects like affine. We show that these models can provide reasonably good estimates with low error bounds for various hardware characteristics of interest and can be a go-to mechanism for hardware cost modelling in the future.

Large language models (LLMs) have achieved significant success across various domains. However, the inherent complexity of causal problems and causal theory poses challenges in accurately describing them in natural language, making it difficult for LLMs to comprehend and use them effectively. Causal methods are not easily conveyed through natural language, which hinders LLMs' ability to apply them accurately. Additionally, causal datasets are typically tabular, while LLMs excel in handling natural language data, creating a structural mismatch that impedes effective reasoning with tabular data. This lack of causal reasoning capability limits the development of LLMs. To address these challenges, we have equipped the LLM with causal tools within an agent framework, named the Causal Agent, enabling it to tackle causal problems. The causal agent comprises tools, memory, and reasoning modules. In the tools module, the causal agent applies causal methods to align tabular data with natural language. In the reasoning module, the causal agent employs the ReAct framework to perform reasoning through multiple iterations with the tools. In the memory module, the causal agent maintains a dictionary instance where the keys are unique names and the values are causal graphs. To verify the causal ability of the causal agent, we established a benchmark consisting of four levels of causal problems: variable level, edge level, causal graph level, and causal effect level. We generated a test dataset of 1.3K using ChatGPT-3.5 for these four levels of issues and tested the causal agent on the datasets. Our methodology demonstrates remarkable efficacy on the four-level causal problems, with accuracy rates all above 80%. For further insights and implementation details, our code is accessible via the GitHub repository https://github.com/Kairong-Han/Causal_Agent.

Graph neural networks have recently achieved remarkable success in representing graph-structured data, with rapid progress in both the node embedding and graph pooling methods. Yet, they mostly focus on capturing information from the nodes considering their connectivity, and not much work has been done in representing the edges, which are essential components of a graph. However, for tasks such as graph reconstruction and generation, as well as graph classification tasks for which the edges are important for discrimination, accurately representing edges of a given graph is crucial to the success of the graph representation learning. To this end, we propose a novel edge representation learning framework based on Dual Hypergraph Transformation (DHT), which transforms the edges of a graph into the nodes of a hypergraph. This dual hypergraph construction allows us to apply message-passing techniques for node representations to edges. After obtaining edge representations from the hypergraphs, we then cluster or drop edges to obtain holistic graph-level edge representations. We validate our edge representation learning method with hypergraphs on diverse graph datasets for graph representation and generation performance, on which our method largely outperforms existing graph representation learning methods. Moreover, our edge representation learning and pooling method also largely outperforms state-of-the-art graph pooling methods on graph classification, not only because of its accurate edge representation learning, but also due to its lossless compression of the nodes and removal of irrelevant edges for effective message-passing.

Contrastive learning has recently achieved remarkable success in many domains including graphs. However contrastive loss, especially for graphs, requires a large number of negative samples which is unscalable and computationally prohibitive with a quadratic time complexity. Sub-sampling is not optimal and incorrect negative sampling leads to sampling bias. In this work, we propose a meta-node based approximation technique that can (a) proxy all negative combinations (b) in quadratic cluster size time complexity, (c) at graph level, not node level, and (d) exploit graph sparsity. By replacing node-pairs with additive cluster-pairs, we compute the negatives in cluster-time at graph level. The resulting Proxy approximated meta-node Contrastive (PamC) loss, based on simple optimized GPU operations, captures the full set of negatives, yet is efficient with a linear time complexity. By avoiding sampling, we effectively eliminate sample bias. We meet the criterion for larger number of samples, thus achieving block-contrastiveness, which is proven to outperform pair-wise losses. We use learnt soft cluster assignments for the meta-node constriction, and avoid possible heterophily and noise added during edge creation. Theoretically, we show that real world graphs easily satisfy conditions necessary for our approximation. Empirically, we show promising accuracy gains over state-of-the-art graph clustering on 6 benchmarks. Importantly, we gain substantially in efficiency; up to 3x in training time, 1.8x in inference time and over 5x in GPU memory reduction.

Recently, many works studied the expressive power of graph neural networks (GNNs) by linking it to the 1-dimensional Weisfeiler--Leman algorithm (1-WL). Here, the 1-WL is a well-studied heuristic for the graph isomorphism problem, which iteratively colors or partitions a graph's vertex set. While this connection has led to significant advances in understanding and enhancing GNNs' expressive power, it does not provide insights into their generalization performance, i.e., their ability to make meaningful predictions beyond the training set. In this paper, we study GNNs' generalization ability through the lens of Vapnik--Chervonenkis (VC) dimension theory in two settings, focusing on graph-level predictions. First, when no upper bound on the graphs' order is known, we show that the bitlength of GNNs' weights tightly bounds their VC dimension. Further, we derive an upper bound for GNNs' VC dimension using the number of colors produced by the 1-WL. Secondly, when an upper bound on the graphs' order is known, we show a tight connection between the number of graphs distinguishable by the 1-WL and GNNs' VC dimension. Our empirical study confirms the validity of our theoretical findings.

Graph Convolutional Networks (GCNs) have shown strong performance in learning text representations for various tasks such as text classification, due to its expressive power in modeling graph structure data (e.g., a literature citation network). Most existing GCNs are limited to deal with documents included in a pre-defined graph, i.e., it cannot be generalized to out-of-graph documents. To address this issue, we propose to transform the document graph into a word graph, to decouple data samples (i.e., documents in training and test sets) and a GCN model by using a document-independent graph. Such word-level GCN could therefore naturally inference out-of-graph documents in an inductive way. The proposed Word-level Graph (WGraph) can not only implicitly learning word presentation with commonly-used word co-occurrences in corpora, but also incorporate extra global semantic dependency derived from inter-document relationships (e.g., literature citations). An inductive Word-grounded Graph Convolutional Network (WGCN) is proposed to learn word and document representations based on WGraph in a supervised manner. Experiments on text classification with and without citation networks evidence that the proposed WGCN model outperforms existing methods in terms of effectiveness and efficiency.

Following the success of Word2Vec embeddings, graph embeddings (GEs) have gained substantial traction. GEs are commonly generated and evaluated extrinsically on downstream applications, but intrinsic evaluations of the original graph properties in terms of topological structure and semantic information have been lacking. Understanding these will help identify the deficiency of the various families of GE methods when vectorizing graphs in terms of preserving the relevant knowledge or learning incorrect knowledge. To address this, we propose RESTORE, a framework for intrinsic GEs assessment through graph reconstruction. We show that reconstructing the original graph from the underlying GEs yields insights into the relative amount of information preserved in a given vector form. We first introduce the graph reconstruction task. We generate GEs from three GE families based on factorization methods, random walks, and deep learning (with representative algorithms from each family) on the CommonSense Knowledge Graph (CSKG). We analyze their effectiveness in preserving the (a) topological structure of node-level graph reconstruction with an increasing number of hops and (b) semantic information on various word semantic and analogy tests. Our evaluations show deep learning-based GE algorithm (SDNE) is overall better at preserving (a) with a mean average precision (mAP) of 0.54 and 0.35 for 2 and 3-hop reconstruction respectively, while the factorization-based algorithm (HOPE) is better at encapsulating (b) with an average Euclidean distance of 0.14, 0.17, and 0.11 for 1, 2, and 3-hop reconstruction respectively. The modest performance of these GEs leaves room for further research avenues on better graph representation learning.

Hyper-relational knowledge graphs (HKGs) extend standard knowledge graphs by associating attribute-value qualifiers to triples, which effectively represent additional fine-grained information about its associated triple. Hyper-relational knowledge graph completion (HKGC) aims at inferring unknown triples while considering its qualifiers. Most existing approaches to HKGC exploit a global-level graph structure to encode hyper-relational knowledge into the graph convolution message passing process. However, the addition of multi-hop information might bring noise into the triple prediction process. To address this problem, we propose HyperFormer, a model that considers local-level sequential information, which encodes the content of the entities, relations and qualifiers of a triple. More precisely, HyperFormer is composed of three different modules: an entity neighbor aggregator module allowing to integrate the information of the neighbors of an entity to capture different perspectives of it; a relation qualifier aggregator module to integrate hyper-relational knowledge into the corresponding relation to refine the representation of relational content; a convolution-based bidirectional interaction module based on a convolutional operation, capturing pairwise bidirectional interactions of entity-relation, entity-qualifier, and relation-qualifier. realize the depth perception of the content related to the current statement. Furthermore, we introduce a Mixture-of-Experts strategy into the feed-forward layers of HyperFormer to strengthen its representation capabilities while reducing the amount of model parameters and computation. Extensive experiments on three well-known datasets with four different conditions demonstrate HyperFormer's effectiveness. Datasets and code are available at https://github.com/zhiweihu1103/HKGC-HyperFormer.

Knowledge graph reasoning (KGR), aiming to deduce new facts from existing facts based on mined logic rules underlying knowledge graphs (KGs), has become a fast-growing research direction. It has been proven to significantly benefit the usage of KGs in many AI applications, such as question answering, recommendation systems, and etc. According to the graph types, existing KGR models can be roughly divided into three categories, i.e., static models, temporal models, and multi-modal models. Early works in this domain mainly focus on static KGR, and recent works try to leverage the temporal and multi-modal information, which are more practical and closer to real-world. However, no survey papers and open-source repositories comprehensively summarize and discuss models in this important direction. To fill the gap, we conduct a first survey for knowledge graph reasoning tracing from static to temporal and then to multi-modal KGs. Concretely, the models are reviewed based on bi-level taxonomy, i.e., top-level (graph types) and base-level (techniques and scenarios). Besides, the performances, as well as datasets, are summarized and presented. Moreover, we point out the challenges and potential opportunities to enlighten the readers. The corresponding open-source repository is shared on GitHub https://github.com/LIANGKE23/Awesome-Knowledge-Graph-Reasoning.

Identification and categorization of social media posts generated during disasters are crucial to reduce the sufferings of the affected people. However, lack of labeled data is a significant bottleneck in learning an effective categorization system for a disaster. This motivates us to study the problem as unsupervised domain adaptation (UDA) between a previous disaster with labeled data (source) and a current disaster (target). However, if the amount of labeled data available is limited, it restricts the learning capabilities of the model. To handle this challenge, we utilize limited labeled data along with abundantly available unlabeled data, generated during a source disaster to propose a novel two-part graph neural network. The first-part extracts domain-agnostic global information by constructing a token level graph across domains and the second-part preserves local instance-level semantics. In our experiments, we show that the proposed method outperforms state-of-the-art techniques by 2.74% weighted F_1 score on average on two standard public dataset in the area of disaster management. We also report experimental results for granular actionable multi-label classification datasets in disaster domain for the first time, on which we outperform BERT by 3.00% on average w.r.t weighted F_1. Additionally, we show that our approach can retain performance when very limited labeled data is available.

Large Language Models (LLMs) have demonstrated remarkable generalization and instruction-following capabilities with instruction tuning. The advancements in LLMs and instruction tuning have led to the development of Large Vision-Language Models (LVLMs). However, the competency of the LLMs and instruction tuning have been less explored in the molecular domain. Thus, we propose LLaMo: Large Language Model-based Molecular graph assistant, which is an end-to-end trained large molecular graph-language model. To bridge the discrepancy between the language and graph modalities, we present the multi-level graph projector that transforms graph representations into graph tokens by abstracting the output representations of each GNN layer and motif representations with the cross-attention mechanism. We also introduce machine-generated molecular graph instruction data to instruction-tune the large molecular graph-language model for general-purpose molecule and language understanding. Our extensive experiments demonstrate that LLaMo shows the best performance on diverse tasks, such as molecular description generation, property prediction, and IUPAC name prediction. The code of LLaMo is available at https://github.com/mlvlab/LLaMo.

Natural reading orders of words are crucial for information extraction from form-like documents. Despite recent advances in Graph Convolutional Networks (GCNs) on modeling spatial layout patterns of documents, they have limited ability to capture reading orders of given word-level node representations in a graph. We propose Reading Order Equivariant Positional Encoding (ROPE), a new positional encoding technique designed to apprehend the sequential presentation of words in documents. ROPE generates unique reading order codes for neighboring words relative to the target word given a word-level graph connectivity. We study two fundamental document entity extraction tasks including word labeling and word grouping on the public FUNSD dataset and a large-scale payment dataset. We show that ROPE consistently improves existing GCNs with a margin up to 8.4% F1-score.

Graph neural network (GNN), as a powerful representation learning model on graph data, attracts much attention across various disciplines. However, recent studies show that GNN is vulnerable to adversarial attacks. How to make GNN more robust? What are the key vulnerabilities in GNN? How to address the vulnerabilities and defense GNN against the adversarial attacks? In this paper, we propose DefNet, an effective adversarial defense framework for GNNs. In particular, we first investigate the latent vulnerabilities in every layer of GNNs and propose corresponding strategies including dual-stage aggregation and bottleneck perceptron. Then, to cope with the scarcity of training data, we propose an adversarial contrastive learning method to train the GNN in a conditional GAN manner by leveraging the high-level graph representation. Extensive experiments on three public datasets demonstrate the effectiveness of DefNet in improving the robustness of popular GNN variants, such as Graph Convolutional Network and GraphSAGE, under various types of adversarial attacks.

Evaluating the performance of a well-trained GNN model on real-world graphs is a pivotal step for reliable GNN online deployment and serving. Due to a lack of test node labels and unknown potential training-test graph data distribution shifts, conventional model evaluation encounters limitations in calculating performance metrics (e.g., test error) and measuring graph data-level discrepancies, particularly when the training graph used for developing GNNs remains unobserved during test time. In this paper, we study a new research problem, online GNN evaluation, which aims to provide valuable insights into the well-trained GNNs's ability to effectively generalize to real-world unlabeled graphs under the test-time graph distribution shifts. Concretely, we develop an effective learning behavior discrepancy score, dubbed LeBeD, to estimate the test-time generalization errors of well-trained GNN models. Through a novel GNN re-training strategy with a parameter-free optimality criterion, the proposed LeBeD comprehensively integrates learning behavior discrepancies from both node prediction and structure reconstruction perspectives. This enables the effective evaluation of the well-trained GNNs' ability to capture test node semantics and structural representations, making it an expressive metric for estimating the generalization error in online GNN evaluation. Extensive experiments on real-world test graphs under diverse graph distribution shifts could verify the effectiveness of the proposed method, revealing its strong correlation with ground-truth test errors on various well-trained GNN models.

Node clustering is a powerful tool in the analysis of networks. We introduce a graph neural network framework, named DIGRAC, to obtain node embeddings for directed networks in a self-supervised manner, including a novel probabilistic imbalance loss, which can be used for network clustering. Here, we propose directed flow imbalance measures, which are tightly related to directionality, to reveal clusters in the network even when there is no density difference between clusters. In contrast to standard approaches in the literature, in this paper, directionality is not treated as a nuisance, but rather contains the main signal. DIGRAC optimizes directed flow imbalance for clustering without requiring label supervision, unlike existing graph neural network methods, and can naturally incorporate node features, unlike existing spectral methods. Extensive experimental results on synthetic data, in the form of directed stochastic block models, and real-world data at different scales, demonstrate that our method, based on flow imbalance, attains state-of-the-art results on directed graph clustering when compared against 10 state-of-the-art methods from the literature, for a wide range of noise and sparsity levels, graph structures, and topologies, and even outperforms supervised methods.

Knowledge distillation is a powerful technique for transferring knowledge from a pre-trained teacher model to a student model. However, the true potential of knowledge transfer has not been fully explored. Existing approaches primarily focus on distilling individual information or instance-level relationships, overlooking the valuable information embedded in token-level relationships, which may be particularly affected by the long-tail effects. To address the above limitations, we propose a novel method called Knowledge Distillation with Token-level Relationship Graph (TRG) that leverages the token-wise relational knowledge to enhance the performance of knowledge distillation. By employing TRG, the student model can effectively emulate higher-level semantic information from the teacher model, resulting in improved distillation results. To further enhance the learning process, we introduce a token-wise contextual loss called contextual loss, which encourages the student model to capture the inner-instance semantic contextual of the teacher model. We conduct experiments to evaluate the effectiveness of the proposed method against several state-of-the-art approaches. Empirical results demonstrate the superiority of TRG across various visual classification tasks, including those involving imbalanced data. Our method consistently outperforms the existing baselines, establishing a new state-of-the-art performance in the field of knowledge distillation.

We present the Power Law Graph Transformer, a transformer model with well defined deductive and inductive tasks for prediction and representation learning. The deductive task learns the dataset level (global) and instance level (local) graph structures in terms of learnable power law distribution parameters. The inductive task outputs the prediction probabilities using the deductive task output, similar to a transductive model. We trained our model with Turkish-English and Portuguese-English datasets from TED talk transcripts for machine translation and compared the model performance and characteristics to a transformer model with scaled dot product attention trained on the same experimental setup. We report BLEU scores of 17.79 and 28.33 on the Turkish-English and Portuguese-English translation tasks with our model, respectively. We also show how a duality between a quantization set and N-dimensional manifold representation can be leveraged to transform between local and global deductive-inductive outputs using successive application of linear and non-linear transformations end-to-end.

The advent of the "pre-train, prompt" paradigm has recently extended its generalization ability and data efficiency to graph representation learning, following its achievements in Natural Language Processing (NLP). Initial graph prompt tuning approaches tailored specialized prompting functions for Graph Neural Network (GNN) models pre-trained with specific strategies, such as edge prediction, thus limiting their applicability. In contrast, another pioneering line of research has explored universal prompting via adding prompts to the input graph's feature space, thereby removing the reliance on specific pre-training strategies. However, the necessity to add feature prompts to all nodes remains an open question. Motivated by findings from prompt tuning research in the NLP domain, which suggest that highly capable pre-trained models need less conditioning signal to achieve desired behaviors, we advocate for strategically incorporating necessary and lightweight feature prompts to certain graph nodes to enhance downstream task performance. This introduces a combinatorial optimization problem, requiring a policy to decide 1) which nodes to prompt and 2) what specific feature prompts to attach. We then address the problem by framing the prompt incorporation process as a sequential decision-making problem and propose our method, RELIEF, which employs Reinforcement Learning (RL) to optimize it. At each step, the RL agent selects a node (discrete action) and determines the prompt content (continuous action), aiming to maximize cumulative performance gain. Extensive experiments on graph and node-level tasks with various pre-training strategies in few-shot scenarios demonstrate that our RELIEF outperforms fine-tuning and other prompt-based approaches in classification performance and data efficiency.

Anatomical segmentation is a fundamental task in medical image computing, generally tackled with fully convolutional neural networks which produce dense segmentation masks. These models are often trained with loss functions such as cross-entropy or Dice, which assume pixels to be independent of each other, thus ignoring topological errors and anatomical inconsistencies. We address this limitation by moving from pixel-level to graph representations, which allow to naturally incorporate anatomical constraints by construction. To this end, we introduce HybridGNet, an encoder-decoder neural architecture that leverages standard convolutions for image feature encoding and graph convolutional neural networks (GCNNs) to decode plausible representations of anatomical structures. We also propose a novel image-to-graph skip connection layer which allows localized features to flow from standard convolutional blocks to GCNN blocks, and show that it improves segmentation accuracy. The proposed architecture is extensively evaluated in a variety of domain shift and image occlusion scenarios, and audited considering different types of demographic domain shift. Our comprehensive experimental setup compares HybridGNet with other landmark and pixel-based models for anatomical segmentation in chest x-ray images, and shows that it produces anatomically plausible results in challenging scenarios where other models tend to fail.

Graph neural networks (GNNs) based methods have achieved impressive performance on node clustering task. However, they are designed on the homophilic assumption of graph and clustering on heterophilic graph is overlooked. Due to the lack of labels, it is impossible to first identify a graph as homophilic or heterophilic before a suitable GNN model can be found. Hence, clustering on real-world graph with various levels of homophily poses a new challenge to the graph research community. To fill this gap, we propose a novel graph clustering method, which contains three key components: graph reconstruction, a mixed filter, and dual graph clustering network. To be graph-agnostic, we empirically construct two graphs which are high homophily and heterophily from each data. The mixed filter based on the new graphs extracts both low-frequency and high-frequency information. To reduce the adverse coupling between node attribute and topological structure, we separately map them into two subspaces in dual graph clustering network. Extensive experiments on 11 benchmark graphs demonstrate our promising performance. In particular, our method dominates others on heterophilic graphs.

3D multimodal question answering (MQA) plays a crucial role in scene understanding by enabling intelligent agents to comprehend their surroundings in 3D environments. While existing research has primarily focused on indoor household tasks and outdoor roadside autonomous driving tasks, there has been limited exploration of city-level scene understanding tasks. Furthermore, existing research faces challenges in understanding city scenes, due to the absence of spatial semantic information and human-environment interaction information at the city level.To address these challenges, we investigate 3D MQA from both dataset and method perspectives. From the dataset perspective, we introduce a novel 3D MQA dataset named City-3DQA for city-level scene understanding, which is the first dataset to incorporate scene semantic and human-environment interactive tasks within the city. From the method perspective, we propose a Scene graph enhanced City-level Understanding method (Sg-CityU), which utilizes the scene graph to introduce the spatial semantic. A new benchmark is reported and our proposed Sg-CityU achieves accuracy of 63.94 % and 63.76 % in different settings of City-3DQA. Compared to indoor 3D MQA methods and zero-shot using advanced large language models (LLMs), Sg-CityU demonstrates state-of-the-art (SOTA) performance in robustness and generalization.

Graph Neural Networks (GNNs) are a popular technique for modelling graph-structured data and computing node-level representations via aggregation of information from the neighborhood of each node. However, this aggregation implies an increased risk of revealing sensitive information, as a node can participate in the inference for multiple nodes. This implies that standard privacy-preserving machine learning techniques, such as differentially private stochastic gradient descent (DP-SGD) - which are designed for situations where each data point participates in the inference for one point only - either do not apply, or lead to inaccurate models. In this work, we formally define the problem of learning GNN parameters with node-level privacy, and provide an algorithmic solution with a strong differential privacy guarantee. We employ a careful sensitivity analysis and provide a non-trivial extension of the privacy-by-amplification technique to the GNN setting. An empirical evaluation on standard benchmark datasets demonstrates that our method is indeed able to learn accurate privacy-preserving GNNs which outperform both private and non-private methods that completely ignore graph information.

In this paper, we study a novel and widely existing problem in graph matching (GM), namely, Bi-level Noisy Correspondence (BNC), which refers to node-level noisy correspondence (NNC) and edge-level noisy correspondence (ENC). In brief, on the one hand, due to the poor recognizability and viewpoint differences between images, it is inevitable to inaccurately annotate some keypoints with offset and confusion, leading to the mismatch between two associated nodes, i.e., NNC. On the other hand, the noisy node-to-node correspondence will further contaminate the edge-to-edge correspondence, thus leading to ENC. For the BNC challenge, we propose a novel method termed Contrastive Matching with Momentum Distillation. Specifically, the proposed method is with a robust quadratic contrastive loss which enjoys the following merits: i) better exploring the node-to-node and edge-to-edge correlations through a GM customized quadratic contrastive learning paradigm; ii) adaptively penalizing the noisy assignments based on the confidence estimated by the momentum teacher. Extensive experiments on three real-world datasets show the robustness of our model compared with 12 competitive baselines. The code is available at https://github.com/XLearning-SCU/2023-ICCV-COMMON.

Optimization problems over dynamic networks have been extensively studied and widely used in the past decades to formulate numerous real-world problems. However, (1) traditional optimization-based approaches do not scale to large networks, and (2) the design of good heuristics or approximation algorithms often requires significant manual trial-and-error. In this work, we argue that data-driven strategies can automate this process and learn efficient algorithms without compromising optimality. To do so, we present network control problems through the lens of reinforcement learning and propose a graph network-based framework to handle a broad class of problems. Instead of naively computing actions over high-dimensional graph elements, e.g., edges, we propose a bi-level formulation where we (1) specify a desired next state via RL, and (2) solve a convex program to best achieve it, leading to drastically improved scalability and performance. We further highlight a collection of desirable features to system designers, investigate design decisions, and present experiments on real-world control problems showing the utility, scalability, and flexibility of our framework.

Most real-world graphs exhibit a hierarchical structure, which is often overlooked by existing graph generation methods. To address this limitation, we propose a novel graph generative network that captures the hierarchical nature of graphs and successively generates the graph sub-structures in a coarse-to-fine fashion. At each level of hierarchy, this model generates communities in parallel, followed by the prediction of cross-edges between communities using separate neural networks. This modular approach enables scalable graph generation for large and complex graphs. Moreover, we model the output distribution of edges in the hierarchical graph with a multinomial distribution and derive a recursive factorization for this distribution. This enables us to generate community graphs with integer-valued edge weights in an autoregressive manner. Empirical studies demonstrate the effectiveness and scalability of our proposed generative model, achieving state-of-the-art performance in terms of graph quality across various benchmark datasets. The code is available at https://github.com/Karami-m/HiGen_main.

We define the bicategory of Graph Convolutional Neural Networks GCNN_n for an arbitrary graph with n nodes. We show it can be factored through the already existing categorical constructions for deep learning called Para and Lens with the base category set to the CoKleisli category of the product comonad. We prove that there exists an injective-on-objects, faithful 2-functor GCNN_n to Para(CoKl(R^{n times n} times -)). We show that this construction allows us to treat the adjacency matrix of a GCNN as a global parameter instead of a a local, layer-wise one. This gives us a high-level categorical characterisation of a particular kind of inductive bias GCNNs possess. Lastly, we hypothesize about possible generalisations of GCNNs to general message-passing graph neural networks, connections to equivariant learning, and the (lack of) functoriality of activation functions.

Intrusion detection system (IDS) is an important part of enterprise security system architecture. In particular, anomaly-based IDS has been widely applied to detect abnormal process behaviors that deviate from the majority. However, such abnormal behavior usually consists of a series of low-level heterogeneous events. The gap between the low-level events and the high-level abnormal behaviors makes it hard to infer which single events are related to the real abnormal activities, especially considering that there are massive "noisy" low-level events happening in between. Hence, the existing work that focus on detecting single entities/events can hardly achieve high detection accuracy. Different from previous work, we design and implement GID, an efficient graph-based intrusion detection technique that can identify abnormal event sequences from a massive heterogeneous process traces with high accuracy. GID first builds a compact graph structure to capture the interactions between different system entities. The suspiciousness or anomaly score of process paths is then measured by leveraging random walk technique to the constructed acyclic directed graph. To eliminate the score bias from the path length, the Box-Cox power transformation based approach is introduced to normalize the anomaly scores so that the scores of paths of different lengths have the same distribution. The efficiency of suspicious path discovery is further improved by the proposed optimization scheme. We fully implement our GID algorithm and deploy it into a real enterprise security system, and it greatly helps detect the advanced threats, and optimize the incident response. Executing GID on system monitoring datasets showing that GID is efficient (about 2 million records per minute) and accurate (higher than 80% in terms of detection rate).

In this paper, we propose Multiresolution Equivariant Graph Variational Autoencoders (MGVAE), the first hierarchical generative model to learn and generate graphs in a multiresolution and equivariant manner. At each resolution level, MGVAE employs higher order message passing to encode the graph while learning to partition it into mutually exclusive clusters and coarsening into a lower resolution that eventually creates a hierarchy of latent distributions. MGVAE then constructs a hierarchical generative model to variationally decode into a hierarchy of coarsened graphs. Importantly, our proposed framework is end-to-end permutation equivariant with respect to node ordering. MGVAE achieves competitive results with several generative tasks including general graph generation, molecular generation, unsupervised molecular representation learning to predict molecular properties, link prediction on citation graphs, and graph-based image generation.

We consider the problem of Human-Object Interaction (HOI) Detection, which aims to locate and recognize HOI instances in the form of <human, action, object> in images. Most existing works treat HOIs as individual interaction categories, thus can not handle the problem of long-tail distribution and polysemy of action labels. We argue that multi-level consistencies among objects, actions and interactions are strong cues for generating semantic representations of rare or previously unseen HOIs. Leveraging the compositional and relational peculiarities of HOI labels, we propose ConsNet, a knowledge-aware framework that explicitly encodes the relations among objects, actions and interactions into an undirected graph called consistency graph, and exploits Graph Attention Networks (GATs) to propagate knowledge among HOI categories as well as their constituents. Our model takes visual features of candidate human-object pairs and word embeddings of HOI labels as inputs, maps them into visual-semantic joint embedding space and obtains detection results by measuring their similarities. We extensively evaluate our model on the challenging V-COCO and HICO-DET datasets, and results validate that our approach outperforms state-of-the-arts under both fully-supervised and zero-shot settings. Code is available at https://github.com/yeliudev/ConsNet.

Prior research on training grounded factuality classification models to detect hallucinations in large language models (LLMs) has relied on public natural language inference (NLI) data and synthetic data. However, conventional NLI datasets are not well-suited for document-level reasoning, which is critical for detecting LLM hallucinations. Recent approaches to document-level synthetic data generation involve iteratively removing sentences from documents and annotating factuality using LLM-based prompts. While effective, this method is computationally expensive for long documents and limited by the LLM's capabilities. In this work, we analyze the differences between existing synthetic training data used in state-of-the-art models and real LLM output claims. Based on our findings, we propose a novel approach for synthetic data generation, CG2C, that leverages multi-hop reasoning on context graphs extracted from documents. Our fact checker model, FactCG, demonstrates improved performance with more connected reasoning, using the same backbone models. Experiments show it even outperforms GPT-4-o on the LLM-Aggrefact benchmark with much smaller model size.

We present an end-to-end deep learning segmentation method by combining a 3D UNet architecture with a graph neural network (GNN) model. In this approach, the convolutional layers at the deepest level of the UNet are replaced by a GNN-based module with a series of graph convolutions. The dense feature maps at this level are transformed into a graph input to the GNN module. The incorporation of graph convolutions in the UNet provides nodes in the graph with information that is based on node connectivity, in addition to the local features learnt through the downsampled paths. This information can help improve segmentation decisions. By stacking several graph convolution layers, the nodes can access higher order neighbourhood information without substantial increase in computational expense. We propose two types of node connectivity in the graph adjacency: i) one predefined and based on a regular node neighbourhood, and ii) one dynamically computed during training and using the nearest neighbour nodes in the feature space. We have applied this method to the task of segmenting the airway tree from chest CT scans. Experiments have been performed on 32 CTs from the Danish Lung Cancer Screening Trial dataset. We evaluate the performance of the UNet-GNN models with two types of graph adjacency and compare it with the baseline UNet.

Ensuring that Software Requirements Specifications (SRS) align with higher-level organizational or national requirements is vital, particularly in regulated environments such as finance and aerospace. In these domains, maintaining consistency, adhering to regulatory frameworks, minimizing errors, and meeting critical expectations are essential for the reliable functioning of systems. The widespread adoption of large language models (LLMs) highlights their immense potential, yet there remains considerable scope for improvement in retrieving relevant information and enhancing reasoning capabilities. This study demonstrates that integrating a robust Graph-RAG framework with advanced prompt engineering techniques, such as Chain of Thought and Tree of Thought, can significantly enhance performance. Compared to baseline RAG methods and simple prompting strategies, this approach delivers more accurate and context-aware results. While this method demonstrates significant improvements in performance, it comes with challenges. It is both costly and more complex to implement across diverse contexts, requiring careful adaptation to specific scenarios. Additionally, its effectiveness heavily relies on having complete and accurate input data, which may not always be readily available, posing further limitations to its scalability and practicality.

This study proposes a hybrid deep-learning-metaheuristic framework with a bi-level architecture for road network design problems (NDPs). We train a graph neural network (GNN) to approximate the solution of the user equilibrium (UE) traffic assignment problem and use inferences made by the trained model to calculate fitness function evaluations of a genetic algorithm (GA) to approximate solutions for NDPs. Using three test networks, two NDP variants and an exact solver as benchmark, we show that on average, our proposed framework can provide solutions within 1.5% gap of the best results in less than 0.5% of the time used by the exact solution procedure. Our framework can be utilized within an expert system for infrastructure planning to determine the best infrastructure planning and management decisions under different scenarios. Given the flexibility of the framework, it can easily be adapted to many other decision problems that can be modeled as bi-level problems on graphs. Moreover, we foreseen interesting future research directions, thus we also put forward a brief research agenda for this topic. The key observation from our research that can shape future research is that the fitness function evaluation time using the inferences made by the GNN model was in the order of milliseconds, which points to an opportunity and a need for novel heuristics that 1) can cope well with noisy fitness function values provided by deep learning models, and 2) can use the significantly enlarged efficiency of the evaluation step to explore the search space effectively (rather than efficiently). This opens a new avenue for a modern class of metaheuristics that are crafted for use with AI-powered predictors.

Accurately predicting road networks from satellite images requires a global understanding of the network topology. We propose to capture such high-level information by introducing a graph-based framework that simulates the addition of sequences of graph edges using a reinforcement learning (RL) approach. In particular, given a partially generated graph associated with a satellite image, an RL agent nominates modifications that maximize a cumulative reward. As opposed to standard supervised techniques that tend to be more restricted to commonly used surrogate losses, these rewards can be based on various complex, potentially non-continuous, metrics of interest. This yields more power and flexibility to encode problem-dependent knowledge. Empirical results on several benchmark datasets demonstrate enhanced performance and increased high-level reasoning about the graph topology when using a tree-based search. We further highlight the superiority of our approach under substantial occlusions by introducing a new synthetic benchmark dataset for this task.

Establishing dense correspondence between two images is a fundamental computer vision problem, which is typically tackled by matching local feature descriptors. However, without global awareness, such local features are often insufficient for disambiguating similar regions. And computing the pairwise feature correlation across images is both computation-expensive and memory-intensive. To make the local features aware of the global context and improve their matching accuracy, we introduce DenseGAP, a new solution for efficient Dense correspondence learning with a Graph-structured neural network conditioned on Anchor Points. Specifically, we first propose a graph structure that utilizes anchor points to provide sparse but reliable prior on inter- and intra-image context and propagates them to all image points via directed edges. We also design a graph-structured network to broadcast multi-level contexts via light-weighted message-passing layers and generate high-resolution feature maps at low memory cost. Finally, based on the predicted feature maps, we introduce a coarse-to-fine framework for accurate correspondence prediction using cycle consistency. Our feature descriptors capture both local and global information, thus enabling a continuous feature field for querying arbitrary points at high resolution. Through comprehensive ablative experiments and evaluations on large-scale indoor and outdoor datasets, we demonstrate that our method advances the state-of-the-art of correspondence learning on most benchmarks.

We report a flexible language-model based deep learning strategy, applied here to solve complex forward and inverse problems in protein modeling, based on an attention neural network that integrates transformer and graph convolutional architectures in a causal multi-headed graph mechanism, to realize a generative pretrained model. The model is applied to predict secondary structure content (per-residue level and overall content), protein solubility, and sequencing tasks. Further trained on inverse tasks, the model is rendered capable of designing proteins with these properties as target features. The model is formulated as a general framework, completely prompt-based, and can be adapted for a variety of downstream tasks. We find that adding additional tasks yields emergent synergies that the model exploits in improving overall performance, beyond what would be possible by training a model on each dataset alone. Case studies are presented to validate the method, yielding protein designs specifically focused on structural proteins, but also exploring the applicability in the design of soluble, antimicrobial biomaterials. While our model is trained to ultimately perform 8 distinct tasks, with available datasets it can be extended to solve additional problems. In a broader sense, this work illustrates a form of multiscale modeling that relates a set of ultimate building blocks (here, byte-level utf8 characters) to complex output. This materiomic scheme captures complex emergent relationships between universal building block and resulting properties via a synergizing learning capacity to express a set of potentialities embedded in the knowledge used in training, via the interplay of universality and diversity.

Given the recent impressive accomplishments of language models (LMs) for code generation, we explore the use of LMs as adaptive mutation and crossover operators for an evolutionary neural architecture search (NAS) algorithm. While NAS still proves too difficult a task for LMs to succeed at solely through prompting, we find that the combination of evolutionary prompt engineering with soft prompt-tuning, a method we term EvoPrompting, consistently finds diverse and high performing models. We first demonstrate that EvoPrompting is effective on the computationally efficient MNIST-1D dataset, where EvoPrompting produces convolutional architecture variants that outperform both those designed by human experts and naive few-shot prompting in terms of accuracy and model size. We then apply our method to searching for graph neural networks on the CLRS Algorithmic Reasoning Benchmark, where EvoPrompting is able to design novel architectures that outperform current state-of-the-art models on 21 out of 30 algorithmic reasoning tasks while maintaining similar model size. EvoPrompting is successful at designing accurate and efficient neural network architectures across a variety of machine learning tasks, while also being general enough for easy adaptation to other tasks beyond neural network design.

We present a novel edge-level ego-network encoding for learning on graphs that can boost Message Passing Graph Neural Networks (MP-GNNs) by providing additional node and edge features or extending message-passing formats. The proposed encoding is sufficient to distinguish Strongly Regular Graphs, a family of challenging 3-WL equivalent graphs. We show theoretically that such encoding is more expressive than node-based sub-graph MP-GNNs. In an empirical evaluation on four benchmarks with 10 graph datasets, our results match or improve previous baselines on expressivity, graph classification, graph regression, and proximity tasks -- while reducing memory usage by 18.1x in certain real-world settings.

In this work we address the problem of landmark-based segmentation for anatomical structures. We propose HybridGNet, an encoder-decoder neural architecture which combines standard convolutions for image feature encoding, with graph convolutional neural networks to decode plausible representations of anatomical structures. We benchmark the proposed architecture considering other standard landmark and pixel-based models for anatomical segmentation in chest x-ray images, and found that HybridGNet is more robust to image occlusions. We also show that it can be used to construct landmark-based segmentations from pixel level annotations. Our experimental results suggest that HybridGNet produces accurate and anatomically plausible landmark-based segmentations, by naturally incorporating shape constraints within the decoding process via spectral convolutions.

We present a novel approach for traffic forecasting in urban traffic scenarios using a combination of spectral graph analysis and deep learning. We predict both the low-level information (future trajectories) as well as the high-level information (road-agent behavior) from the extracted trajectory of each road-agent. Our formulation represents the proximity between the road agents using a weighted dynamic geometric graph (DGG). We use a two-stream graph-LSTM network to perform traffic forecasting using these weighted DGGs. The first stream predicts the spatial coordinates of road-agents, while the second stream predicts whether a road-agent is going to exhibit overspeeding, underspeeding, or neutral behavior by modeling spatial interactions between road-agents. Additionally, we propose a new regularization algorithm based on spectral clustering to reduce the error margin in long-term prediction (3-5 seconds) and improve the accuracy of the predicted trajectories. Moreover, we prove a theoretical upper bound on the regularized prediction error. We evaluate our approach on the Argoverse, Lyft, Apolloscape, and NGSIM datasets and highlight the benefits over prior trajectory prediction methods. In practice, our approach reduces the average prediction error by approximately 75% over prior algorithms and achieves a weighted average accuracy of 91.2% for behavior prediction. Additionally, our spectral regularization improves long-term prediction by up to 70%.

Vision-based sign language recognition aims at helping deaf people to communicate with others. However, most existing sign language datasets are limited to a small number of words. Due to the limited vocabulary size, models learned from those datasets cannot be applied in practice. In this paper, we introduce a new large-scale Word-Level American Sign Language (WLASL) video dataset, containing more than 2000 words performed by over 100 signers. This dataset will be made publicly available to the research community. To our knowledge, it is by far the largest public ASL dataset to facilitate word-level sign recognition research. Based on this new large-scale dataset, we are able to experiment with several deep learning methods for word-level sign recognition and evaluate their performances in large scale scenarios. Specifically we implement and compare two different models,i.e., (i) holistic visual appearance-based approach, and (ii) 2D human pose based approach. Both models are valuable baselines that will benefit the community for method benchmarking. Moreover, we also propose a novel pose-based temporal graph convolution networks (Pose-TGCN) that models spatial and temporal dependencies in human pose trajectories simultaneously, which has further boosted the performance of the pose-based method. Our results show that pose-based and appearance-based models achieve comparable performances up to 66% at top-10 accuracy on 2,000 words/glosses, demonstrating the validity and challenges of our dataset. Our dataset and baseline deep models are available at https://dxli94.github.io/WLASL/.

Object categories are typically organized into a multi-granularity taxonomic hierarchy. When classifying categories at different hierarchy levels, traditional uni-modal approaches focus primarily on image features, revealing limitations in complex scenarios. Recent studies integrating Vision-Language Models (VLMs) with class hierarchies have shown promise, yet they fall short of fully exploiting the hierarchical relationships. These efforts are constrained by their inability to perform effectively across varied granularity of categories. To tackle this issue, we propose a novel framework (HGCLIP) that effectively combines CLIP with a deeper exploitation of the Hierarchical class structure via Graph representation learning. We explore constructing the class hierarchy into a graph, with its nodes representing the textual or image features of each category. After passing through a graph encoder, the textual features incorporate hierarchical structure information, while the image features emphasize class-aware features derived from prototypes through the attention mechanism. Our approach demonstrates significant improvements on 11 diverse visual recognition benchmarks. Our codes are fully available at https://github.com/richard-peng-xia/HGCLIP.

Many real-world systems exhibit temporal, dynamic behaviors, which are captured as time series of complex agent interactions. To perform temporal reasoning, current methods primarily encode temporal dynamics through simple sequence-based models. However, in general these models fail to efficiently capture the full spectrum of rich dynamics in the input, since the dynamics is not uniformly distributed. In particular, relevant information might be harder to extract and computing power is wasted for processing all individual timesteps, even if they contain no significant changes or no new information. Here we propose TimeGraphs, a novel approach that characterizes dynamic interactions as a hierarchical temporal graph, diverging from traditional sequential representations. Our approach models the interactions using a compact graph-based representation, enabling adaptive reasoning across diverse time scales. Adopting a self-supervised method, TimeGraphs constructs a multi-level event hierarchy from a temporal input, which is then used to efficiently reason about the unevenly distributed dynamics. This construction process is scalable and incremental to accommodate streaming data. We evaluate TimeGraphs on multiple datasets with complex, dynamic agent interactions, including a football simulator, the Resistance game, and the MOMA human activity dataset. The results demonstrate both robustness and efficiency of TimeGraphs on a range of temporal reasoning tasks. Our approach obtains state-of-the-art performance and leads to a performance increase of up to 12.2% on event prediction and recognition tasks over current approaches. Our experiments further demonstrate a wide array of capabilities including zero-shot generalization, robustness in case of data sparsity, and adaptability to streaming data flow.

Recent developments in retrieval-augmented generation (RAG) for selecting relevant tools from a tool knowledge base enable LLM agents to scale their complex tool calling capabilities to hundreds or thousands of external tools, APIs, or agents-as-tools. However, traditional RAG-based tool retrieval fails to capture structured dependencies between tools, limiting the retrieval accuracy of a retrieved tool's dependencies. For example, among a vector database of tools, a "get stock price" API requires a "stock ticker" parameter from a "get stock ticker" API, and both depend on OS-level internet connectivity tools. In this paper, we address this limitation by introducing Graph RAG-Tool Fusion, a novel plug-and-play approach that combines the strengths of vector-based retrieval with efficient graph traversal to capture all relevant tools (nodes) along with any nested dependencies (edges) within the predefined tool knowledge graph. We also present ToolLinkOS, a new tool selection benchmark of 573 fictional tools, spanning over 15 industries, each with an average of 6.3 tool dependencies. We demonstrate that Graph RAG-Tool Fusion achieves absolute improvements of 71.7% and 22.1% over na\"ive RAG on ToolLinkOS and ToolSandbox benchmarks, respectively (mAP@10). ToolLinkOS dataset is available at https://github.com/EliasLumer/Graph-RAG-Tool-Fusion-ToolLinkOS

Scene graphs offer a structured, hierarchical representation of images, with nodes and edges symbolizing objects and the relationships among them. It can serve as a natural interface for image editing, dramatically improving precision and flexibility. Leveraging this benefit, we introduce a new framework that integrates large language model (LLM) with Text2Image generative model for scene graph-based image editing. This integration enables precise modifications at the object level and creative recomposition of scenes without compromising overall image integrity. Our approach involves two primary stages: 1) Utilizing a LLM-driven scene parser, we construct an image's scene graph, capturing key objects and their interrelationships, as well as parsing fine-grained attributes such as object masks and descriptions. These annotations facilitate concept learning with a fine-tuned diffusion model, representing each object with an optimized token and detailed description prompt. 2) During the image editing phase, a LLM editing controller guides the edits towards specific areas. These edits are then implemented by an attention-modulated diffusion editor, utilizing the fine-tuned model to perform object additions, deletions, replacements, and adjustments. Through extensive experiments, we demonstrate that our framework significantly outperforms existing image editing methods in terms of editing precision and scene aesthetics.

In this paper, we propose a novel method for joint entity and relation extraction from unstructured text by framing it as a conditional sequence generation problem. In contrast to conventional generative information extraction models that are left-to-right token-level generators, our approach is span-based. It generates a linearized graph where nodes represent text spans and edges represent relation triplets. Our method employs a transformer encoder-decoder architecture with pointing mechanism on a dynamic vocabulary of spans and relation types. Our model can capture the structural characteristics and boundaries of entities and relations through span representations while simultaneously grounding the generated output in the original text thanks to the pointing mechanism. Evaluation on benchmark datasets validates the effectiveness of our approach, demonstrating competitive results. Code is available at https://github.com/urchade/ATG.

We study graph data augmentation by mixup, which has been used successfully on images. A key operation of mixup is to compute a convex combination of a pair of inputs. This operation is straightforward for grid-like data, such as images, but challenging for graph data. The key difficulty lies in the fact that different graphs typically have different numbers of nodes, and thus there lacks a node-level correspondence between graphs. In this work, we propose S-Mixup, a simple yet effective mixup method for graph classification by soft alignments. Specifically, given a pair of graphs, we explicitly obtain node-level correspondence via computing a soft assignment matrix to match the nodes between two graphs. Based on the soft assignments, we transform the adjacency and node feature matrices of one graph, so that the transformed graph is aligned with the other graph. In this way, any pair of graphs can be mixed directly to generate an augmented graph. We conduct systematic experiments to show that S-Mixup can improve the performance and generalization of graph neural networks (GNNs) on various graph classification tasks. In addition, we show that S-Mixup can increase the robustness of GNNs against noisy labels.

Explaining node predictions in graph neural networks (GNNs) often boils down to finding graph substructures that preserve predictions. Finding these structures usually implies back-propagating through the GNN, bonding the complexity (e.g., number of layers) of the GNN to the cost of explaining it. This naturally begs the question: Can we break this bond by explaining a simpler surrogate GNN? To answer the question, we propose Distill n' Explain (DnX). First, DnX learns a surrogate GNN via knowledge distillation. Then, DnX extracts node or edge-level explanations by solving a simple convex program. We also propose FastDnX, a faster version of DnX that leverages the linear decomposition of our surrogate model. Experiments show that DnX and FastDnX often outperform state-of-the-art GNN explainers while being orders of magnitude faster. Additionally, we support our empirical findings with theoretical results linking the quality of the surrogate model (i.e., distillation error) to the faithfulness of explanations.

Predicting diverse human motions given a sequence of historical poses has received increasing attention. Despite rapid progress, existing work captures the multi-modal nature of human motions primarily through likelihood-based sampling, where the mode collapse has been widely observed. In this paper, we propose a simple yet effective approach that disentangles randomly sampled codes with a deterministic learnable component named anchors to promote sample precision and diversity. Anchors are further factorized into spatial anchors and temporal anchors, which provide attractively interpretable control over spatial-temporal disparity. In principle, our spatial-temporal anchor-based sampling (STARS) can be applied to different motion predictors. Here we propose an interaction-enhanced spatial-temporal graph convolutional network (IE-STGCN) that encodes prior knowledge of human motions (e.g., spatial locality), and incorporate the anchors into it. Extensive experiments demonstrate that our approach outperforms state of the art in both stochastic and deterministic prediction, suggesting it as a unified framework for modeling human motions. Our code and pretrained models are available at https://github.com/Sirui-Xu/STARS.

Conversational semantic role labeling (CSRL) is a newly proposed task that uncovers the shallow semantic structures in a dialogue text. Unfortunately several important characteristics of the CSRL task have been overlooked by the existing works, such as the structural information integration, near-neighbor influence. In this work, we investigate the integration of a latent graph for CSRL. We propose to automatically induce a predicate-oriented latent graph (POLar) with a predicate-centered Gaussian mechanism, by which the nearer and informative words to the predicate will be allocated with more attention. The POLar structure is then dynamically pruned and refined so as to best fit the task need. We additionally introduce an effective dialogue-level pre-trained language model, CoDiaBERT, for better supporting multiple utterance sentences and handling the speaker coreference issue in CSRL. Our system outperforms best-performing baselines on three benchmark CSRL datasets with big margins, especially achieving over 4% F1 score improvements on the cross-utterance argument detection. Further analyses are presented to better understand the effectiveness of our proposed methods.

Graphs are a powerful tool for representing and analyzing complex relationships in real-world applications such as social networks, recommender systems, and computational finance. Reasoning on graphs is essential for drawing inferences about the relationships between entities in a complex system, and to identify hidden patterns and trends. Despite the remarkable progress in automated reasoning with natural text, reasoning on graphs with large language models (LLMs) remains an understudied problem. In this work, we perform the first comprehensive study of encoding graph-structured data as text for consumption by LLMs. We show that LLM performance on graph reasoning tasks varies on three fundamental levels: (1) the graph encoding method, (2) the nature of the graph task itself, and (3) interestingly, the very structure of the graph considered. These novel results provide valuable insight on strategies for encoding graphs as text. Using these insights we illustrate how the correct choice of encoders can boost performance on graph reasoning tasks inside LLMs by 4.8% to 61.8%, depending on the task.

Feature selection is playing an increasingly significant role with respect to many computer vision applications spanning from object recognition to visual object tracking. However, most of the recent solutions in feature selection are not robust across different and heterogeneous set of data. In this paper, we address this issue proposing a robust probabilistic latent graph-based feature selection algorithm that performs the ranking step while considering all the possible subsets of features, as paths on a graph, bypassing the combinatorial problem analytically. An appealing characteristic of the approach is that it aims to discover an abstraction behind low-level sensory data, that is, relevancy. Relevancy is modelled as a latent variable in a PLSA-inspired generative process that allows the investigation of the importance of a feature when injected into an arbitrary set of cues. The proposed method has been tested on ten diverse benchmarks, and compared against eleven state of the art feature selection methods. Results show that the proposed approach attains the highest performance levels across many different scenarios and difficulties, thereby confirming its strong robustness while setting a new state of the art in feature selection domain.

Post-Training Quantization (PTQ) is pivotal for deploying large language models (LLMs) within resource-limited settings by significantly reducing resource demands. However, existing PTQ strategies underperform at low bit levels < 3 bits due to the significant difference between the quantized and original weights. To enhance the quantization performance at low bit widths, we introduce a Mixed-precision Graph Neural PTQ (MG-PTQ) approach, employing a graph neural network (GNN) module to capture dependencies among weights and adaptively assign quantization bit-widths. Through the information propagation of the GNN module, our method more effectively captures dependencies among target weights, leading to a more accurate assessment of weight importance and optimized allocation of quantization strategies. Extensive experiments on the WikiText2 and C4 datasets demonstrate that our MG-PTQ method outperforms previous state-of-the-art PTQ method GPTQ, setting new benchmarks for quantization performance under low-bit conditions.

Biomedical knowledge is uniquely complex and structured, requiring distinct reasoning strategies compared to other scientific disciplines like physics or chemistry. Biomedical scientists do not rely on a single approach to reasoning; instead, they use various strategies, including rule-based, prototype-based, and case-based reasoning. This diversity calls for flexible approaches that accommodate multiple reasoning strategies while leveraging in-domain knowledge. We introduce KGARevion, a knowledge graph (KG) based agent designed to address the complexity of knowledge-intensive medical queries. Upon receiving a query, KGARevion generates relevant triplets by using the knowledge base of the LLM. These triplets are then verified against a grounded KG to filter out erroneous information and ensure that only accurate, relevant data contribute to the final answer. Unlike RAG-based models, this multi-step process ensures robustness in reasoning while adapting to different models of medical reasoning. Evaluations on four gold-standard medical QA datasets show that KGARevion improves accuracy by over 5.2%, outperforming 15 models in handling complex medical questions. To test its capabilities, we curated three new medical QA datasets with varying levels of semantic complexity, where KGARevion achieved a 10.4% improvement in accuracy.

This study introduces a parameter-efficient Hierarchical Spatial Temporal Network (HiSTN) specifically designed for the task of emotion classification using multi-channel electroencephalogram data. The network incorporates a graph hierarchy constructed from bottom-up at various abstraction levels, offering the dual advantages of enhanced task-relevant deep feature extraction and a lightweight design. The model's effectiveness is further amplified when used in conjunction with a proposed unique label smoothing method. Comprehensive benchmark experiments reveal that this combined approach yields high, balanced performance in terms of both quantitative and qualitative predictions. HiSTN, which has approximately 1,000 parameters, achieves mean F1 scores of 96.82% (valence) and 95.62% (arousal) in subject-dependent tests on the rarely-utilized 5-classification task problem from the DREAMER dataset. In the subject-independent settings, the same model yields mean F1 scores of 78.34% for valence and 81.59% for arousal. The adoption of the Sequential Top-2 Hit Rate (Seq2HR) metric highlights the significant enhancements in terms of the balance between model's quantitative and qualitative for predictions achieved through our approach when compared to training with regular one-hot labels. These improvements surpass 50% in subject-dependent tasks and 30% in subject-independent tasks. The study also includes relevant ablation studies and case explorations to further elucidate the workings of the proposed model and enhance its interpretability.

Graphs can be leveraged to model polyphonic multitrack symbolic music, where notes, chords and entire sections may be linked at different levels of the musical hierarchy by tonal and rhythmic relationships. Nonetheless, there is a lack of works that consider graph representations in the context of deep learning systems for music generation. This paper bridges this gap by introducing a novel graph representation for music and a deep Variational Autoencoder that generates the structure and the content of musical graphs separately, one after the other, with a hierarchical architecture that matches the structural priors of music. By separating the structure and content of musical graphs, it is possible to condition generation by specifying which instruments are played at certain times. This opens the door to a new form of human-computer interaction in the context of music co-creation. After training the model on existing MIDI datasets, the experiments show that the model is able to generate appealing short and long musical sequences and to realistically interpolate between them, producing music that is tonally and rhythmically consistent. Finally, the visualization of the embeddings shows that the model is able to organize its latent space in accordance with known musical concepts.

Many real-world user queries (e.g. "How do to make egg fried rice?") could benefit from systems capable of generating responses with both textual steps with accompanying images, similar to a cookbook. Models designed to generate interleaved text and images face challenges in ensuring consistency within and across these modalities. To address these challenges, we present ISG, a comprehensive evaluation framework for interleaved text-and-image generation. ISG leverages a scene graph structure to capture relationships between text and image blocks, evaluating responses on four levels of granularity: holistic, structural, block-level, and image-specific. This multi-tiered evaluation allows for a nuanced assessment of consistency, coherence, and accuracy, and provides interpretable question-answer feedback. In conjunction with ISG, we introduce a benchmark, ISG-Bench, encompassing 1,150 samples across 8 categories and 21 subcategories. This benchmark dataset includes complex language-vision dependencies and golden answers to evaluate models effectively on vision-centric tasks such as style transfer, a challenging area for current models. Using ISG-Bench, we demonstrate that recent unified vision-language models perform poorly on generating interleaved content. While compositional approaches that combine separate language and image models show a 111% improvement over unified models at the holistic level, their performance remains suboptimal at both block and image levels. To facilitate future work, we develop ISG-Agent, a baseline agent employing a "plan-execute-refine" pipeline to invoke tools, achieving a 122% performance improvement.

Dialogue-based Role Playing Games (RPGs) require powerful storytelling. The narratives of these may take years to write and typically involve a large creative team. In this work, we demonstrate the potential of large generative text models to assist this process. GRIM, a prototype GRaph-based Interactive narrative visualization system for gaMes, generates a rich narrative graph with branching storylines that match a high-level narrative description and constraints provided by the designer. Game designers can interactively edit the graph by automatically generating new sub-graphs that fit the edits within the original narrative and constraints. We illustrate the use of GRIM in conjunction with GPT-4, generating branching narratives for four well-known stories with different contextual constraints.

We present an agentic, autonomous graph expansion framework that iteratively structures and refines knowledge in situ. Unlike conventional knowledge graph construction methods relying on static extraction or single-pass learning, our approach couples a reasoning-native large language model with a continually updated graph representation. At each step, the system actively generates new concepts and relationships, merges them into a global graph, and formulates subsequent prompts based on its evolving structure. Through this feedback-driven loop, the model organizes information into a scale-free network characterized by hub formation, stable modularity, and bridging nodes that link disparate knowledge clusters. Over hundreds of iterations, new nodes and edges continue to appear without saturating, while centrality measures and shortest path distributions evolve to yield increasingly distributed connectivity. Our analysis reveals emergent patterns, such as the rise of highly connected 'hub' concepts and the shifting influence of 'bridge' nodes, indicating that agentic, self-reinforcing graph construction can yield open-ended, coherent knowledge structures. Applied to materials design problems, we present compositional reasoning experiments by extracting node-specific and synergy-level principles to foster genuinely novel knowledge synthesis, yielding cross-domain ideas that transcend rote summarization and strengthen the framework's potential for open-ended scientific discovery. We discuss other applications in scientific discovery and outline future directions for enhancing scalability and interpretability.

Robots are increasingly being used in dynamic environments like workplaces, hospitals, and homes. As a result, interactions with robots must be simple and intuitive, with robots perception adapting efficiently to human-induced changes. This paper presents a robot control architecture that addresses key challenges in human-robot interaction, with a particular focus on the dynamic creation and continuous update of the robot state representation. The architecture uses Large Language Models to integrate diverse information sources, including natural language commands, robotic skills representation, real-time dynamic semantic mapping of the perceived scene. This enables flexible and adaptive robotic behavior in complex, dynamic environments. Traditional robotic systems often rely on static, pre-programmed instructions and settings, limiting their adaptability to dynamic environments and real-time collaboration. In contrast, this architecture uses LLMs to interpret complex, high-level instructions and generate actionable plans that enhance human-robot collaboration. At its core, the system Perception Module generates and continuously updates a semantic scene graph using RGB-D sensor data, providing a detailed and structured representation of the environment. A particle filter is employed to ensure accurate object localization in dynamic, real-world settings. The Planner Module leverages this up-to-date semantic map to break down high-level tasks into sub-tasks and link them to robotic skills such as navigation, object manipulation (e.g., PICK and PLACE), and movement (e.g., GOTO). By combining real-time perception, state tracking, and LLM-driven communication and task planning, the architecture enhances adaptability, task efficiency, and human-robot collaboration in dynamic environments.

Spatio-Temporal Graph (STG) forecasting is a fundamental task in many real-world applications. Spatio-Temporal Graph Neural Networks have emerged as the most popular method for STG forecasting, but they often struggle with temporal out-of-distribution (OoD) issues and dynamic spatial causation. In this paper, we propose a novel framework called CaST to tackle these two challenges via causal treatments. Concretely, leveraging a causal lens, we first build a structural causal model to decipher the data generation process of STGs. To handle the temporal OoD issue, we employ the back-door adjustment by a novel disentanglement block to separate invariant parts and temporal environments from input data. Moreover, we utilize the front-door adjustment and adopt the Hodge-Laplacian operator for edge-level convolution to model the ripple effect of causation. Experiments results on three real-world datasets demonstrate the effectiveness and practicality of CaST, which consistently outperforms existing methods with good interpretability.

This study introduces a novel framework, G3Reg, for fast and robust global registration of LiDAR point clouds. In contrast to conventional complex keypoints and descriptors, we extract fundamental geometric primitives, including planes, clusters, and lines (PCL) from the raw point cloud to obtain low-level semantic segments. Each segment is represented as a unified Gaussian Ellipsoid Model (GEM), using a probability ellipsoid to ensure the ground truth centers are encompassed with a certain degree of probability. Utilizing these GEMs, we present a distrust-and-verify scheme based on a Pyramid Compatibility Graph for Global Registration (PAGOR). Specifically, we establish an upper bound, which can be traversed based on the confidence level for compatibility testing to construct the pyramid graph. Then, we solve multiple maximum cliques (MAC) for each level of the pyramid graph, thus generating the corresponding transformation candidates. In the verification phase, we adopt a precise and efficient metric for point cloud alignment quality, founded on geometric primitives, to identify the optimal candidate. The algorithm's performance is validated on three publicly available datasets and a self-collected multi-session dataset. Parameter settings remained unchanged during the experiment evaluations. The results exhibit superior robustness and real-time performance of the G3Reg framework compared to state-of-the-art methods. Furthermore, we demonstrate the potential for integrating individual GEM and PAGOR components into other registration frameworks to enhance their efficacy. Code: https://github.com/HKUST-Aerial-Robotics/G3Reg

We present the Temporal Graph Benchmark (TGB), a collection of challenging and diverse benchmark datasets for realistic, reproducible, and robust evaluation of machine learning models on temporal graphs. TGB datasets are of large scale, spanning years in duration, incorporate both node and edge-level prediction tasks and cover a diverse set of domains including social, trade, transaction, and transportation networks. For both tasks, we design evaluation protocols based on realistic use-cases. We extensively benchmark each dataset and find that the performance of common models can vary drastically across datasets. In addition, on dynamic node property prediction tasks, we show that simple methods often achieve superior performance compared to existing temporal graph models. We believe that these findings open up opportunities for future research on temporal graphs. Finally, TGB provides an automated machine learning pipeline for reproducible and accessible temporal graph research, including data loading, experiment setup and performance evaluation. TGB will be maintained and updated on a regular basis and welcomes community feedback. TGB datasets, data loaders, example codes, evaluation setup, and leaderboards are publicly available at https://tgb.complexdatalab.com/.

Emotion Support Conversation (ESC) is an emerging and challenging task with the goal of reducing the emotional distress of people. Previous attempts fail to maintain smooth transitions between utterances in ESC because they ignore to grasp the fine-grained transition information at each dialogue turn. To solve this problem, we propose to take into account turn-level state Transitions of ESC (TransESC) from three perspectives, including semantics transition, strategy transition and emotion transition, to drive the conversation in a smooth and natural way. Specifically, we construct the state transition graph with a two-step way, named transit-then-interact, to grasp such three types of turn-level transition information. Finally, they are injected into the transition-aware decoder to generate more engaging responses. Both automatic and human evaluations on the benchmark dataset demonstrate the superiority of TransESC to generate more smooth and effective supportive responses. Our source code is available at https://github.com/circle-hit/TransESC.

Molecular relational learning, whose goal is to learn the interaction behavior between molecular pairs, got a surge of interest in molecular sciences due to its wide range of applications. Recently, graph neural networks have recently shown great success in molecular relational learning by modeling a molecule as a graph structure, and considering atom-level interactions between two molecules. Despite their success, existing molecular relational learning methods tend to overlook the nature of chemistry, i.e., a chemical compound is composed of multiple substructures such as functional groups that cause distinctive chemical reactions. In this work, we propose a novel relational learning framework, called CGIB, that predicts the interaction behavior between a pair of graphs by detecting core subgraphs therein. The main idea is, given a pair of graphs, to find a subgraph from a graph that contains the minimal sufficient information regarding the task at hand conditioned on the paired graph based on the principle of conditional graph information bottleneck. We argue that our proposed method mimics the nature of chemical reactions, i.e., the core substructure of a molecule varies depending on which other molecule it interacts with. Extensive experiments on various tasks with real-world datasets demonstrate the superiority of CGIB over state-of-the-art baselines. Our code is available at https://github.com/Namkyeong/CGIB.

In this paper, we propose REASON, a novel framework that enables the automatic discovery of both intra-level (i.e., within-network) and inter-level (i.e., across-network) causal relationships for root cause localization. REASON consists of Topological Causal Discovery and Individual Causal Discovery. The Topological Causal Discovery component aims to model the fault propagation in order to trace back to the root causes. To achieve this, we propose novel hierarchical graph neural networks to construct interdependent causal networks by modeling both intra-level and inter-level non-linear causal relations. Based on the learned interdependent causal networks, we then leverage random walks with restarts to model the network propagation of a system fault. The Individual Causal Discovery component focuses on capturing abrupt change patterns of a single system entity. This component examines the temporal patterns of each entity's metric data (i.e., time series), and estimates its likelihood of being a root cause based on the Extreme Value theory. Combining the topological and individual causal scores, the top K system entities are identified as root causes. Extensive experiments on three real-world datasets with case studies demonstrate the effectiveness and superiority of the proposed framework.

Graph Neural Networks (GNNs) have greatly advanced the semi-supervised node classification task on graphs. The majority of existing GNNs are trained in an end-to-end manner that can be viewed as tackling a bi-level optimization problem. This process is often inefficient in computation and memory usage. In this work, we propose a new optimization framework for semi-supervised learning on graphs. The proposed framework can be conveniently solved by the alternating optimization algorithms, resulting in significantly improved efficiency. Extensive experiments demonstrate that the proposed method can achieve comparable or better performance with state-of-the-art baselines while it has significantly better computation and memory efficiency.

Contrastive pretraining techniques for text classification has been largely studied in an unsupervised setting. However, oftentimes labeled data from related tasks which share label semantics with current task is available. We hypothesize that using this labeled data effectively can lead to better generalization on current task. In this paper, we propose a novel way to effectively utilize labeled data from related tasks with a graph based supervised contrastive learning approach. We formulate a token-graph by extrapolating the supervised information from examples to tokens. Our formulation results in an embedding space where tokens with high/low probability of belonging to same class are near/further-away from one another. We also develop detailed theoretical insights which serve as a motivation for our method. In our experiments with 13 datasets, we show our method outperforms pretraining schemes by 2.5% and also example-level contrastive learning based formulation by 1.8% on average. In addition, we show cross-domain effectiveness of our method in a zero-shot setting by 3.91% on average. Lastly, we also demonstrate our method can be used as a noisy teacher in a knowledge distillation setting to significantly improve performance of transformer based models in low labeled data regime by 4.57% on average.

Representation learning on heterogeneous graphs aims to obtain meaningful node representations to facilitate various downstream tasks, such as node classification and link prediction. Existing heterogeneous graph learning methods are primarily developed by following the propagation mechanism of node representations. There are few efforts on studying the role of relations for improving the learning of more fine-grained node representations. Indeed, it is important to collaboratively learn the semantic representations of relations and discern node representations with respect to different relation types. To this end, in this paper, we propose a novel Relation-aware Heterogeneous Graph Neural Network, namely R-HGNN, to learn node representations on heterogeneous graphs at a fine-grained level by considering relation-aware characteristics. Specifically, a dedicated graph convolution component is first designed to learn unique node representations from each relation-specific graph separately. Then, a cross-relation message passing module is developed to improve the interactions of node representations across different relations. Also, the relation representations are learned in a layer-wise manner to capture relation semantics, which are used to guide the node representation learning process. Moreover, a semantic fusing module is presented to aggregate relation-aware node representations into a compact representation with the learned relation representations. Finally, we conduct extensive experiments on a variety of graph learning tasks, and experimental results demonstrate that our approach consistently outperforms existing methods among all the tasks.

This paper presents DWIE, the 'Deutsche Welle corpus for Information Extraction', a newly created multi-task dataset that combines four main Information Extraction (IE) annotation subtasks: (i) Named Entity Recognition (NER), (ii) Coreference Resolution, (iii) Relation Extraction (RE), and (iv) Entity Linking. DWIE is conceived as an entity-centric dataset that describes interactions and properties of conceptual entities on the level of the complete document. This contrasts with currently dominant mention-driven approaches that start from the detection and classification of named entity mentions in individual sentences. Further, DWIE presented two main challenges when building and evaluating IE models for it. First, the use of traditional mention-level evaluation metrics for NER and RE tasks on entity-centric DWIE dataset can result in measurements dominated by predictions on more frequently mentioned entities. We tackle this issue by proposing a new entity-driven metric that takes into account the number of mentions that compose each of the predicted and ground truth entities. Second, the document-level multi-task annotations require the models to transfer information between entity mentions located in different parts of the document, as well as between different tasks, in a joint learning setting. To realize this, we propose to use graph-based neural message passing techniques between document-level mention spans. Our experiments show an improvement of up to 5.5 F1 percentage points when incorporating neural graph propagation into our joint model. This demonstrates DWIE's potential to stimulate further research in graph neural networks for representation learning in multi-task IE. We make DWIE publicly available at https://github.com/klimzaporojets/DWIE.

Recent studies on Graph Convolutional Networks (GCNs) reveal that the initial node representations (i.e., the node representations before the first-time graph convolution) largely affect the final model performance. However, when learning the initial representation for a node, most existing work linearly combines the embeddings of node features, without considering the interactions among the features (or feature embeddings). We argue that when the node features are categorical, e.g., in many real-world applications like user profiling and recommender system, feature interactions usually carry important signals for predictive analytics. Ignoring them will result in suboptimal initial node representation and thus weaken the effectiveness of the follow-up graph convolution. In this paper, we propose a new GCN model named CatGCN, which is tailored for graph learning when the node features are categorical. Specifically, we integrate two ways of explicit interaction modeling into the learning of initial node representation, i.e., local interaction modeling on each pair of node features and global interaction modeling on an artificial feature graph. We then refine the enhanced initial node representations with the neighborhood aggregation-based graph convolution. We train CatGCN in an end-to-end fashion and demonstrate it on semi-supervised node classification. Extensive experiments on three tasks of user profiling (the prediction of user age, city, and purchase level) from Tencent and Alibaba datasets validate the effectiveness of CatGCN, especially the positive effect of performing feature interaction modeling before graph convolution.

Point clouds provide a flexible geometric representation suitable for countless applications in computer graphics; they also comprise the raw output of most 3D data acquisition devices. While hand-designed features on point clouds have long been proposed in graphics and vision, however, the recent overwhelming success of convolutional neural networks (CNNs) for image analysis suggests the value of adapting insight from CNN to the point cloud world. Point clouds inherently lack topological information so designing a model to recover topology can enrich the representation power of point clouds. To this end, we propose a new neural network module dubbed EdgeConv suitable for CNN-based high-level tasks on point clouds including classification and segmentation. EdgeConv acts on graphs dynamically computed in each layer of the network. It is differentiable and can be plugged into existing architectures. Compared to existing modules operating in extrinsic space or treating each point independently, EdgeConv has several appealing properties: It incorporates local neighborhood information; it can be stacked applied to learn global shape properties; and in multi-layer systems affinity in feature space captures semantic characteristics over potentially long distances in the original embedding. We show the performance of our model on standard benchmarks including ModelNet40, ShapeNetPart, and S3DIS.

With the web getting bigger and assimilating knowledge about different concepts and domains, it is becoming very difficult for simple database driven applications to capture the data for a domain. Thus developers have come out with ontology based systems which can store large amount of information and can apply reasoning and produce timely information. Thus facilitating effective knowledge management. Though this approach has made our lives easier, but at the same time has given rise to another problem. Two different ontologies assimilating same knowledge tend to use different terms for the same concepts. This creates confusion among knowledge engineers and workers, as they do not know which is a better term then the other. Thus we need to merge ontologies working on same domain so that the engineers can develop a better application over it. This paper shows the development of one such matcher which merges the concepts available in two ontologies at two levels; 1) at string level and 2) at semantic level; thus producing better merged ontologies. We have used a graph matching technique which works at the core of the system. We have also evaluated the system and have tested its performance with its predecessor which works only on string matching. Thus current approach produces better results.

Deep graph clustering has recently received significant attention due to its ability to enhance the representation learning capabilities of models in unsupervised scenarios. Nevertheless, deep clustering for temporal graphs, which could capture crucial dynamic interaction information, has not been fully explored. It means that in many clustering-oriented real-world scenarios, temporal graphs can only be processed as static graphs. This not only causes the loss of dynamic information but also triggers huge computational consumption. To solve the problem, we propose a general framework for deep Temporal Graph Clustering called TGC, which introduces deep clustering techniques to suit the interaction sequence-based batch-processing pattern of temporal graphs. In addition, we discuss differences between temporal graph clustering and static graph clustering from several levels. To verify the superiority of the proposed framework TGC, we conduct extensive experiments. The experimental results show that temporal graph clustering enables more flexibility in finding a balance between time and space requirements, and our framework can effectively improve the performance of existing temporal graph learning methods. The code is released: https://github.com/MGitHubL/Deep-Temporal-Graph-Clustering.

Event extraction is a classic task in natural language processing with wide use in handling large amount of yet rapidly growing financial, legal, medical, and government documents which often contain multiple events with their elements scattered and mixed across the documents, making the problem much more difficult. Though the underlying relations between event elements to be extracted provide helpful contextual information, they are somehow overlooked in prior studies. We showcase the enhancement to this task brought by utilizing the knowledge graph that captures entity relations and their attributes. We propose a first event extraction framework that embeds a knowledge graph through a Graph Neural Network and integrates the embedding with regular features, all at document-level. Specifically, for extracting events from Chinese financial announcements, our method outperforms the state-of-the-art method by 5.3% in F1-score.

Graph representation learning nowadays becomes fundamental in analyzing graph-structured data. Inspired by recent success of contrastive methods, in this paper, we propose a novel framework for unsupervised graph representation learning by leveraging a contrastive objective at the node level. Specifically, we generate two graph views by corruption and learn node representations by maximizing the agreement of node representations in these two views. To provide diverse node contexts for the contrastive objective, we propose a hybrid scheme for generating graph views on both structure and attribute levels. Besides, we provide theoretical justification behind our motivation from two perspectives, mutual information and the classical triplet loss. We perform empirical experiments on both transductive and inductive learning tasks using a variety of real-world datasets. Experimental experiments demonstrate that despite its simplicity, our proposed method consistently outperforms existing state-of-the-art methods by large margins. Moreover, our unsupervised method even surpasses its supervised counterparts on transductive tasks, demonstrating its great potential in real-world applications.

Language models have been effective in a wide range of applications, yet the most sophisticated models are often proprietary. For example, GPT-4 by OpenAI and various models by Anthropic are expensive and consume substantial energy. In contrast, the open-source community has produced competitive models, like Llama3. Furthermore, niche-specific smaller language models, such as those tailored for legal, medical or financial tasks, have outperformed their proprietary counterparts. This paper introduces a novel approach that employs functional tokens to integrate multiple open-source models, each optimized for particular tasks. Our newly developed Octopus v4 model leverages functional tokens to intelligently direct user queries to the most appropriate vertical model and reformat the query to achieve the best performance. Octopus v4, an evolution of the Octopus v1, v2, and v3 models, excels in selection and parameter understanding and reformatting. Additionally, we explore the use of graph as a versatile data structure that effectively coordinates multiple open-source models by harnessing the capabilities of the Octopus model and functional tokens. Use our open-sourced GitHub (https://www.nexa4ai.com/) to try Octopus v4 models (https://huggingface.co/NexaAIDev/Octopus-v4), and contrite to a larger graph of language models. By activating models less than 10B parameters, we achieved SOTA MMLU score of 74.8 among the same level models.

Towards building comprehensive real-world visual perception systems, we propose and study a new problem called panoptic scene graph generation (PVSG). PVSG relates to the existing video scene graph generation (VidSGG) problem, which focuses on temporal interactions between humans and objects grounded with bounding boxes in videos. However, the limitation of bounding boxes in detecting non-rigid objects and backgrounds often causes VidSGG to miss key details crucial for comprehensive video understanding. In contrast, PVSG requires nodes in scene graphs to be grounded by more precise, pixel-level segmentation masks, which facilitate holistic scene understanding. To advance research in this new area, we contribute the PVSG dataset, which consists of 400 videos (289 third-person + 111 egocentric videos) with a total of 150K frames labeled with panoptic segmentation masks as well as fine, temporal scene graphs. We also provide a variety of baseline methods and share useful design practices for future work.

In the midst of widespread misinformation and disinformation through social media and the proliferation of AI-generated texts, it has become increasingly difficult for people to validate and trust information they encounter. Many fact-checking approaches and tools have been developed, but they often lack appropriate explainability or granularity to be useful in various contexts. A text validation method that is easy to use, accessible, and can perform fine-grained evidence attribution has become crucial. More importantly, building user trust in such a method requires presenting the rationale behind each prediction, as research shows this significantly influences people's belief in automated systems. It is also paramount to localize and bring users' attention to the specific problematic content, instead of providing simple blanket labels. In this paper, we present ClaimVer, a human-centric framework tailored to meet users' informational and verification needs by generating rich annotations and thereby reducing cognitive load. Designed to deliver comprehensive evaluations of texts, it highlights each claim, verifies it against a trusted knowledge graph (KG), presents the evidence, and provides succinct, clear explanations for each claim prediction. Finally, our framework introduces an attribution score, enhancing applicability across a wide range of downstream tasks.

Knowledge graphs (KGs) generated by large language models (LLMs) are becoming increasingly valuable for Retrieval-Augmented Generation (RAG) applications that require knowledge-intensive reasoning. However, existing KG extraction methods predominantly rely on prompt-based approaches, which are inefficient for processing large-scale corpora. These approaches often suffer from information loss, particularly with long documents, due to the lack of specialized design for KG construction. Additionally, there is a gap in evaluation datasets and methodologies for ontology-free KG construction. To overcome these limitations, we propose SynthKG, a multi-step, document-level ontology-free KG synthesis workflow based on LLMs. By fine-tuning a smaller LLM on the synthesized document-KG pairs, we streamline the multi-step process into a single-step KG generation approach called Distill-SynthKG, substantially reducing the number of LLM inference calls. Furthermore, we re-purpose existing question-answering datasets to establish KG evaluation datasets and introduce new evaluation metrics. Using KGs produced by Distill-SynthKG, we also design a novel graph-based retrieval framework for RAG. Experimental results demonstrate that Distill-SynthKG not only surpasses all baseline models in KG quality -- including models up to eight times larger -- but also consistently excels in retrieval and question-answering tasks. Our proposed graph retrieval framework also outperforms all KG-retrieval methods across multiple benchmark datasets. We release the SynthKG dataset and Distill-SynthKG model publicly to support further research and development.

This paper presents a pilot study aimed at introducing multi-agent debate into multimodal reasoning. The study addresses two key challenges: the trivialization of opinions resulting from excessive summarization and the diversion of focus caused by distractor concepts introduced from images. These challenges stem from the inductive (bottom-up) nature of existing debating schemes. To address the issue, we propose a deductive (top-down) debating approach called Blueprint Debate on Graphs (BDoG). In BDoG, debates are confined to a blueprint graph to prevent opinion trivialization through world-level summarization. Moreover, by storing evidence in branches within the graph, BDoG mitigates distractions caused by frequent but irrelevant concepts. Extensive experiments validate that BDoG is able to achieve state-of-the-art results in ScienceQA and MMBench with significant improvements over previous methods. The source code can be accessed at https://github.com/thecharm/BDoG.

Posterior sampling allows the exploitation of prior knowledge of the environment's transition dynamics to improve the sample efficiency of reinforcement learning. The prior is typically specified as a class of parametric distributions, a task that can be cumbersome in practice, often resulting in the choice of uninformative priors. In this work, we propose a novel posterior sampling approach in which the prior is given as a (partial) causal graph over the environment's variables. The latter is often more natural to design, such as listing known causal dependencies between biometric features in a medical treatment study. Specifically, we propose a hierarchical Bayesian procedure, called C-PSRL, simultaneously learning the full causal graph at the higher level and the parameters of the resulting factored dynamics at the lower level. For this procedure, we provide an analysis of its Bayesian regret, which explicitly connects the regret rate with the degree of prior knowledge. Our numerical evaluation conducted in illustrative domains confirms that C-PSRL strongly improves the efficiency of posterior sampling with an uninformative prior while performing close to posterior sampling with the full causal graph.

Recent years have seen a growing interest in Scene Graph Generation (SGG), a comprehensive visual scene understanding task that aims to predict entity relationships using a relation encoder-decoder pipeline stacked on top of an object encoder-decoder backbone. Unfortunately, current SGG methods suffer from an information loss regarding the entities local-level cues during the relation encoding process. To mitigate this, we introduce the Vision rElation TransfOrmer (VETO), consisting of a novel local-level entity relation encoder. We further observe that many existing SGG methods claim to be unbiased, but are still biased towards either head or tail classes. To overcome this bias, we introduce a Mutually Exclusive ExperT (MEET) learning strategy that captures important relation features without bias towards head or tail classes. Experimental results on the VG and GQA datasets demonstrate that VETO + MEET boosts the predictive performance by up to 47 percentage over the state of the art while being 10 times smaller.

Class prototype construction and matching are core aspects of few-shot action recognition. Previous methods mainly focus on designing spatiotemporal relation modeling modules or complex temporal alignment algorithms. Despite the promising results, they ignored the value of class prototype construction and matching, leading to unsatisfactory performance in recognizing similar categories in every task. In this paper, we propose GgHM, a new framework with Graph-guided Hybrid Matching. Concretely, we learn task-oriented features by the guidance of a graph neural network during class prototype construction, optimizing the intra- and inter-class feature correlation explicitly. Next, we design a hybrid matching strategy, combining frame-level and tuple-level matching to classify videos with multivariate styles. We additionally propose a learnable dense temporal modeling module to enhance the video feature temporal representation to build a more solid foundation for the matching process. GgHM shows consistent improvements over other challenging baselines on several few-shot datasets, demonstrating the effectiveness of our method. The code will be publicly available at https://github.com/jiazheng-xing/GgHM.

Weakly-supervised temporal action localization (WTAL) is a practical yet challenging task. Due to large-scale datasets, most existing methods use a network pretrained in other datasets to extract features, which are not suitable enough for WTAL. To address this problem, researchers design several modules for feature enhancement, which improve the performance of the localization module, especially modeling the temporal relationship between snippets. However, all of them neglect the adverse effects of ambiguous information, which would reduce the discriminability of others. Considering this phenomenon, we propose Discriminability-Driven Graph Network (DDG-Net), which explicitly models ambiguous snippets and discriminative snippets with well-designed connections, preventing the transmission of ambiguous information and enhancing the discriminability of snippet-level representations. Additionally, we propose feature consistency loss to prevent the assimilation of features and drive the graph convolution network to generate more discriminative representations. Extensive experiments on THUMOS14 and ActivityNet1.2 benchmarks demonstrate the effectiveness of DDG-Net, establishing new state-of-the-art results on both datasets. Source code is available at https://github.com/XiaojunTang22/ICCV2023-DDGNet.

DL compiler's primary function is to translate DNN programs written in high-level DL frameworks such as PyTorch and TensorFlow into portable executables. These executables can then be flexibly executed by the deployed host programs. However, existing DL compilers rely on a tracing mechanism, which involves feeding a runtime input to a neural network program and tracing the program execution paths to generate the computational graph necessary for compilation. Unfortunately, this mechanism falls short when dealing with modern dynamic neural networks (DyNNs) that possess varying computational graphs depending on the inputs. Consequently, conventional DL compilers struggle to accurately compile DyNNs into executable code. To address this limitation, we propose \tool, a general approach that enables any existing DL compiler to successfully compile DyNNs. \tool tackles the dynamic nature of DyNNs by introducing a compilation mechanism that redistributes the control and data flow of the original DNN programs during the compilation process. Specifically, \tool develops program analysis and program transformation techniques to convert a dynamic neural network into multiple sub-neural networks. Each sub-neural network is devoid of conditional statements and is compiled independently. Furthermore, \tool synthesizes a host module that models the control flow of the DyNNs and facilitates the invocation of the sub-neural networks. Our evaluation demonstrates the effectiveness of \tool, achieving a 100\% success rate in compiling all dynamic neural networks. Moreover, the compiled executables generated by \tool exhibit significantly improved performance, running between 1.12times and 20.21times faster than the original DyNNs executed on general-purpose DL frameworks.

Given the importance of getting calibrated predictions and reliable uncertainty estimations, various post-hoc calibration methods have been developed for neural networks on standard multi-class classification tasks. However, these methods are not well suited for calibrating graph neural networks (GNNs), which presents unique challenges such as accounting for the graph structure and the graph-induced correlations between the nodes. In this work, we conduct a systematic study on the calibration qualities of GNN node predictions. In particular, we identify five factors which influence the calibration of GNNs: general under-confident tendency, diversity of nodewise predictive distributions, distance to training nodes, relative confidence level, and neighborhood similarity. Furthermore, based on the insights from this study, we design a novel calibration method named Graph Attention Temperature Scaling (GATS), which is tailored for calibrating graph neural networks. GATS incorporates designs that address all the identified influential factors and produces nodewise temperature scaling using an attention-based architecture. GATS is accuracy-preserving, data-efficient, and expressive at the same time. Our experiments empirically verify the effectiveness of GATS, demonstrating that it can consistently achieve state-of-the-art calibration results on various graph datasets for different GNN backbones.

Knowledge Graphs, such as Wikidata, comprise structural and textual knowledge in order to represent knowledge. For each of the two modalities dedicated approaches for graph embedding and language models learn patterns that allow for predicting novel structural knowledge. Few approaches have integrated learning and inference with both modalities and these existing ones could only partially exploit the interaction of structural and textual knowledge. In our approach, we build on existing strong representations of single modalities and we use hypercomplex algebra to represent both, (i), single-modality embedding as well as, (ii), the interaction between different modalities and their complementary means of knowledge representation. More specifically, we suggest Dihedron and Quaternion representations of 4D hypercomplex numbers to integrate four modalities namely structural knowledge graph embedding, word-level representations (e.g.\ Word2vec, Fasttext), sentence-level representations (Sentence transformer), and document-level representations (sentence transformer, Doc2vec). Our unified vector representation scores the plausibility of labelled edges via Hamilton and Dihedron products, thus modeling pairwise interactions between different modalities. Extensive experimental evaluation on standard benchmark datasets shows the superiority of our two new models using abundant textual information besides sparse structural knowledge to enhance performance in link prediction tasks.

Controllable 3D scene generation has extensive applications in virtual reality and interior design, where the generated scenes should exhibit high levels of realism and controllability in terms of geometry. Scene graphs provide a suitable data representation that facilitates these applications. However, current graph-based methods for scene generation are constrained to text-based inputs and exhibit insufficient adaptability to flexible user inputs, hindering the ability to precisely control object geometry. To address this issue, we propose MMGDreamer, a dual-branch diffusion model for scene generation that incorporates a novel Mixed-Modality Graph, visual enhancement module, and relation predictor. The mixed-modality graph allows object nodes to integrate textual and visual modalities, with optional relationships between nodes. It enhances adaptability to flexible user inputs and enables meticulous control over the geometry of objects in the generated scenes. The visual enhancement module enriches the visual fidelity of text-only nodes by constructing visual representations using text embeddings. Furthermore, our relation predictor leverages node representations to infer absent relationships between nodes, resulting in more coherent scene layouts. Extensive experimental results demonstrate that MMGDreamer exhibits superior control of object geometry, achieving state-of-the-art scene generation performance. Project page: https://yangzhifeio.github.io/project/MMGDreamer.

3D vision-language (VL) reasoning has gained significant attention due to its potential to bridge the 3D physical world with natural language descriptions. Existing approaches typically follow task-specific, highly specialized paradigms. Therefore, these methods focus on a limited range of reasoning sub-tasks and rely heavily on the hand-crafted modules and auxiliary losses. This highlights the need for a simpler, unified and general-purpose model. In this paper, we leverage the inherent connection between 3D scene graphs and natural language, proposing a 3D scene graph-guided vision-language pre-training (VLP) framework. Our approach utilizes modality encoders, graph convolutional layers and cross-attention layers to learn universal representations that adapt to a variety of 3D VL reasoning tasks, thereby eliminating the need for task-specific designs. The pre-training objectives include: 1) Scene graph-guided contrastive learning, which leverages the strong correlation between 3D scene graphs and natural language to align 3D objects with textual features at various fine-grained levels; and 2) Masked modality learning, which uses cross-modality information to reconstruct masked words and 3D objects. Instead of directly reconstructing the 3D point clouds of masked objects, we use position clues to predict their semantic categories. Extensive experiments demonstrate that our pre-training model, when fine-tuned on several downstream tasks, achieves performance comparable to or better than existing methods in tasks such as 3D visual grounding, 3D dense captioning, and 3D question answering.

Discovering novel drug candidate molecules is one of the most fundamental and critical steps in drug development. Generative deep learning models, which create synthetic data given a probability distribution, have been developed with the purpose of picking completely new samples from a partially known space. Generative models offer high potential for designing de novo molecules; however, in order for them to be useful in real-life drug development pipelines, these models should be able to design target-specific molecules, which is the next step in this field. In this study, we propose DrugGEN, for the de novo design of drug candidate molecules that interact with selected target proteins. The proposed system represents compounds and protein structures as graphs and processes them via serially connected two generative adversarial networks comprising graph transformers. DrugGEN is trained using a large dataset of compounds from ChEMBL and target-specific bioactive molecules, to design effective and specific inhibitory molecules against the AKT1 protein, which has critical importance for developing treatments against various types of cancer. On fundamental benchmarks, DrugGEN models have either competitive or better performance against other methods. To assess the target-specific generation performance, we conducted further in silico analysis with molecular docking and deep learning-based bioactivity prediction. Results indicate that de novo molecules have high potential for interacting with the AKT1 protein structure in the level of its native ligand. DrugGEN can be used to design completely novel and effective target-specific drug candidate molecules for any druggable protein, given target features and a dataset of experimental bioactivities. Code base, datasets, results and trained models of DrugGEN are available at https://github.com/HUBioDataLab/DrugGEN

Graph-to-text generation has benefited from pre-trained language models (PLMs) in achieving better performance than structured graph encoders. However, they fail to fully utilize the structure information of the input graph. In this paper, we aim to further improve the performance of the pre-trained language model by proposing a structured graph-to-text model with a two-step fine-tuning mechanism which first fine-tunes the model on Wikipedia before adapting to the graph-to-text generation. In addition to using the traditional token and position embeddings to encode the knowledge graph (KG), we propose a novel tree-level embedding method to capture the inter-dependency structures of the input graph. This new approach has significantly improved the performance of all text generation metrics for the English WebNLG 2017 dataset.

In numerous artificial intelligence applications, the collaborative efforts of multiple intelligent agents are imperative for the successful attainment of target objectives. To enhance coordination among these agents, a distributed communication framework is often employed. However, indiscriminate information sharing among all agents can be resource-intensive, and the adoption of manually pre-defined communication architectures imposes constraints on inter-agent communication, thus limiting the potential for effective collaboration. Moreover, the communication framework often remains static during inference, which may result in sustained high resource consumption, as in most cases, only key decisions necessitate information sharing among agents. In this study, we introduce a novel approach wherein we conceptualize the communication architecture among agents as a learnable graph. We formulate this problem as the task of determining the communication graph while enabling the architecture parameters to update normally, thus necessitating a bi-level optimization process. Utilizing continuous relaxation of the graph representation and incorporating attention units, our proposed approach, CommFormer, efficiently optimizes the communication graph and concurrently refines architectural parameters through gradient descent in an end-to-end manner. Additionally, we introduce a temporal gating mechanism for each agent, enabling dynamic decisions on whether to receive shared information at a given time, based on current observations, thus improving decision-making efficiency. Extensive experiments on a variety of cooperative tasks substantiate the robustness of our model across diverse cooperative scenarios, where agents are able to develop more coordinated and sophisticated strategies regardless of changes in the number of agents.

Heterophilic Graph Neural Networks (HGNNs) have shown promising results for semi-supervised learning tasks on graphs. Notably, most real-world heterophilic graphs are composed of a mixture of nodes with different neighbor patterns, exhibiting local node-level homophilic and heterophilic structures. However, existing works are only devoted to designing better HGNN backbones or architectures for node classification tasks on heterophilic and homophilic graph benchmarks simultaneously, and their analyses of HGNN performance with respect to nodes are only based on the determined data distribution without exploring the effect caused by this structural difference between training and testing nodes. How to learn invariant node representations on heterophilic graphs to handle this structure difference or distribution shifts remains unexplored. In this paper, we first discuss the limitations of previous graph-based invariant learning methods from the perspective of data augmentation. Then, we propose HEI, a framework capable of generating invariant node representations through incorporating heterophily information to infer latent environments without augmentation, which are then used for invariant prediction, under heterophilic graph structure distribution shifts. We theoretically show that our proposed method can achieve guaranteed performance under heterophilic graph structure distribution shifts. Extensive experiments on various benchmarks and backbones can also demonstrate the effectiveness of our method compared with existing state-of-the-art baselines.

Detecting anomalies is important for identifying inefficiencies, errors, or fraud in business processes. Traditional process mining approaches focus on analyzing 'flattened', sequential, event logs based on a single case notion. However, many real-world process executions exhibit a graph-like structure, where events can be associated with multiple cases. Flattening event logs requires selecting a single case identifier which creates a gap with the real event data and artificially introduces anomalies in the event logs. Object-centric process mining avoids these limitations by allowing events to be related to different cases. This study proposes a novel framework for anomaly detection in business processes that exploits graph neural networks and the enhanced information offered by object-centric process mining. We first reconstruct and represent the process dependencies of the object-centric event logs as attributed graphs and then employ a graph convolutional autoencoder architecture to detect anomalous events. Our results show that our approach provides promising performance in detecting anomalies at the activity type and attributes level, although it struggles to detect anomalies in the temporal order of events.

Molecular structure recognition is the task of translating a molecular image into its graph structure. Significant variation in drawing styles and conventions exhibited in chemical literature poses a significant challenge for automating this task. In this paper, we propose MolScribe, a novel image-to-graph generation model that explicitly predicts atoms and bonds, along with their geometric layouts, to construct the molecular structure. Our model flexibly incorporates symbolic chemistry constraints to recognize chirality and expand abbreviated structures. We further develop data augmentation strategies to enhance the model robustness against domain shifts. In experiments on both synthetic and realistic molecular images, MolScribe significantly outperforms previous models, achieving 76-93% accuracy on public benchmarks. Chemists can also easily verify MolScribe's prediction, informed by its confidence estimation and atom-level alignment with the input image. MolScribe is publicly available through Python and web interfaces: https://github.com/thomas0809/MolScribe.

Large language models (LLMs) have achieved impressive success across several fields, but their proficiency in understanding and resolving complex graph problems is less explored. To bridge this gap, we introduce GraphInstruct, a novel and comprehensive instruction-tuning dataset designed to equip language models with the ability to tackle a broad spectrum of graph problems using explicit reasoning paths. Utilizing GraphInstruct, we build GraphWiz, an open-source language model capable of resolving various graph problem types while generating clear reasoning processes. To enhance the model's capability and reliability, we incorporate the Direct Preference Optimization (DPO) framework into the graph problem-solving context. The enhanced model, GraphWiz-DPO, achieves an average accuracy of 65% across nine tasks with different complexity levels, surpassing GPT-4 which has an average accuracy of 43.8%. Moreover, our research delves into the delicate balance between training data volume and model performance, highlighting the potential for overfitting with increased data. We also explore the transferability of the model's reasoning ability across different graph tasks, indicating the model's adaptability and practical application potential. Our investigation offers a new blueprint and valuable insights for developing LLMs specialized in graph reasoning and problem-solving.

The angular synchronization problem aims to accurately estimate (up to a constant additive phase) a set of unknown angles theta_1, dots, theta_nin[0, 2pi) from m noisy measurements of their offsets theta_i-theta_j ;mod ; 2pi. Applications include, for example, sensor network localization, phase retrieval, and distributed clock synchronization. An extension of the problem to the heterogeneous setting (dubbed k-synchronization) is to estimate k groups of angles simultaneously, given noisy observations (with unknown group assignment) from each group. Existing methods for angular synchronization usually perform poorly in high-noise regimes, which are common in applications. In this paper, we leverage neural networks for the angular synchronization problem, and its heterogeneous extension, by proposing GNNSync, a theoretically-grounded end-to-end trainable framework using directed graph neural networks. In addition, new loss functions are devised to encode synchronization objectives. Experimental results on extensive data sets demonstrate that GNNSync attains competitive, and often superior, performance against a comprehensive set of baselines for the angular synchronization problem and its extension, validating the robustness of GNNSync even at high noise levels.

Although Large Language Models (LLMs) have demonstrated potential in processing graphs, they struggle with comprehending graphical structure information through prompts of graph description sequences, especially as the graph size increases. We attribute this challenge to the uneven memory performance of LLMs across different positions in graph description sequences, known as ''positional biases''. To address this, we propose GraphInsight, a novel framework aimed at improving LLMs' comprehension of both macro- and micro-level graphical information. GraphInsight is grounded in two key strategies: 1) placing critical graphical information in positions where LLMs exhibit stronger memory performance, and 2) investigating a lightweight external knowledge base for regions with weaker memory performance, inspired by retrieval-augmented generation (RAG). Moreover, GraphInsight explores integrating these two strategies into LLM agent processes for composite graph tasks that require multi-step reasoning. Extensive empirical studies on benchmarks with a wide range of evaluation tasks show that GraphInsight significantly outperforms all other graph description methods (e.g., prompting techniques and reordering strategies) in understanding graph structures of varying sizes.

Medical visual question answering (VQA) aims to answer clinically relevant questions regarding input medical images. This technique has the potential to improve the efficiency of medical professionals while relieving the burden on the public health system, particularly in resource-poor countries. Existing medical VQA methods tend to encode medical images and learn the correspondence between visual features and questions without exploiting the spatial, semantic, or medical knowledge behind them. This is partially because of the small size of the current medical VQA dataset, which often includes simple questions. Therefore, we first collected a comprehensive and large-scale medical VQA dataset, focusing on chest X-ray images. The questions involved detailed relationships, such as disease names, locations, levels, and types in our dataset. Based on this dataset, we also propose a novel baseline method by constructing three different relationship graphs: spatial relationship, semantic relationship, and implicit relationship graphs on the image regions, questions, and semantic labels. The answer and graph reasoning paths are learned for different questions.

The need to analyze graphs is ubiquitous across various fields, from social networks to biological research and recommendation systems. Therefore, enabling the ability of large language models (LLMs) to process graphs is an important step toward more advanced general intelligence. However, current LLM benchmarks on graph analysis require models to directly reason over the prompts describing graph topology, and are thus limited to small graphs with only a few dozens of nodes. In contrast, human experts typically write programs based on popular libraries for task solving, and can thus handle graphs with different scales. To this end, a question naturally arises: can LLMs analyze graphs like professionals? In this paper, we introduce ProGraph, a manually crafted benchmark containing 3 categories of graph tasks. The benchmark expects solutions based on programming instead of directly reasoning over raw inputs. Our findings reveal that the performance of current LLMs is unsatisfactory, with the best model achieving only 36% accuracy. To bridge this gap, we propose LLM4Graph datasets, which include crawled documents and auto-generated codes based on 6 widely used graph libraries. By augmenting closed-source LLMs with document retrieval and fine-tuning open-source ones on the codes, we show 11-32% absolute improvements in their accuracies. Our results underscore that the capabilities of LLMs in handling structured data are still under-explored, and show the effectiveness of LLM4Graph in enhancing LLMs' proficiency of graph analysis. The benchmark, datasets and enhanced open-source models are available at https://github.com/BUPT-GAMMA/ProGraph.

Relational graph neural networks (RGNNs) are graph neural networks (GNNs) with dedicated structures for modeling the different types of nodes and/or edges in heterogeneous graphs. While RGNNs have been increasingly adopted in many real-world applications due to their versatility and accuracy, they pose performance and system design challenges due to their inherent computation patterns, gap between the programming interface and kernel APIs, and heavy programming efforts in optimizing kernels caused by their coupling with data layout and heterogeneity. To systematically address these challenges, we propose Pigeon, a novel two-level intermediate representation (IR) and its code generator framework, that (a) represents the key properties of the RGNN models to bridge the gap between the programming interface and kernel APIs, (b) decouples model semantics, data layout, and operators-specific optimization from each other to reduce programming efforts, (c) expresses and leverages optimization opportunities in inter-operator transforms, data layout, and operator-specific schedules. By building on one general matrix multiply (GEMM) template and a node/edge traversal template, Pigeon achieves up to 7.8x speed-up in inference and 5.6x speed-up in training compared with the state-of-the-art public systems in select models, i.e., RGCN, RGAT, HGT, when running heterogeneous graphs provided by Deep Graph Library (DGL) and Open Graph Benchmark (OGB). Pigeon also triggers fewer out-of-memory (OOM) errors. In addition, we propose linear operator fusion and compact materialization to further accelerate the system by up to 2.2x.

Large language models (LLMs) have demonstrated remarkable success across a wide range of tasks; however, they still encounter challenges in reasoning tasks that require understanding and inferring relationships between distinct pieces of information within text sequences. This challenge is particularly pronounced in tasks involving multi-step processes, such as logical reasoning and multi-hop question answering, where understanding implicit relationships between entities and leveraging multi-hop connections in the given context are crucial. Graphs, as fundamental data structures, explicitly represent pairwise relationships between entities, thereby offering the potential to enhance LLMs' reasoning capabilities. External graphs have proven effective in supporting LLMs across multiple tasks. However, in many reasoning tasks, no pre-existing graph structure is provided. Can we structure implicit knowledge derived from context into graphs to assist LLMs in reasoning? In this paper, we propose Reasoning with Graphs (RwG) by first constructing explicit graphs from the context and then leveraging these graphs to enhance LLM reasoning performance on reasoning tasks. Extensive experiments demonstrate the effectiveness of the proposed method in improving both logical reasoning and multi-hop question answering tasks.

With the emergence of data marketplaces, the demand for methods to assess the value of data has increased significantly. While numerous techniques have been proposed for this purpose, none have specifically addressed graphs as the main data modality. Graphs are widely used across various fields, ranging from chemical molecules to social networks. In this study, we break down graphs into two main components: structural and featural, and we focus on evaluating data without relying on specific task-related metrics, making it applicable in practical scenarios where validation requirements may be lacking. We introduce a novel framework called blind message passing, which aligns the seller's and buyer's graphs using a shared node permutation based on graph matching. This allows us to utilize the graph Wasserstein distance to quantify the differences in the structural distribution of graph datasets, called the structural disparities. We then consider featural aspects of buyers' and sellers' graphs for data valuation and capture their statistical similarities and differences, referred to as relevance and diversity, respectively. Our approach ensures that buyers and sellers remain unaware of each other's datasets. Our experiments on real datasets demonstrate the effectiveness of our approach in capturing the relevance, diversity, and structural disparities of seller data for buyers, particularly in graph-based data valuation scenarios.

Various human-designed prompt engineering techniques have been proposed to improve problem solvers based on Large Language Models (LLMs), yielding many disparate code bases. We unify these approaches by describing LLM-based agents as computational graphs. The nodes implement functions to process multimodal data or query LLMs, and the edges describe the information flow between operations. Graphs can be recursively combined into larger composite graphs representing hierarchies of inter-agent collaboration (where edges connect operations of different agents). Our novel automatic graph optimizers (1) refine node-level LLM prompts (node optimization) and (2) improve agent orchestration by changing graph connectivity (edge optimization). Experiments demonstrate that our framework can be used to efficiently develop, integrate, and automatically improve various LLM agents. The code can be found at https://github.com/metauto-ai/gptswarm.

Designing a single model to address multiple tasks has been a long-standing objective in artificial intelligence. Recently, large language models have demonstrated exceptional capability in solving different tasks within the language domain. However, a unified model for various graph tasks remains underexplored, primarily due to the challenges unique to the graph learning domain. First, graph data from different areas carry distinct attributes and follow different distributions. Such discrepancy makes it hard to represent graphs in a single representation space. Second, tasks on graphs diversify into node, link, and graph tasks, requiring distinct embedding strategies. Finally, an appropriate graph prompting paradigm for in-context learning is unclear. We propose One for All (OFA), the first general framework that can use a single graph model to address the above challenges. Specifically, OFA proposes text-attributed graphs to unify different graph data by describing nodes and edges with natural language and uses language models to encode the diverse and possibly cross-domain text attributes to feature vectors in the same embedding space. Furthermore, OFA introduces the concept of nodes-of-interest to standardize different tasks with a single task representation. For in-context learning on graphs, OFA introduces a novel graph prompting paradigm that appends prompting substructures to the input graph, which enables it to address varied tasks without fine-tuning. We train the OFA model using graph data from multiple domains (including citation networks, molecular graphs, knowledge graphs, etc.) simultaneously and evaluate its ability in supervised, few-shot, and zero-shot learning scenarios. OFA performs well across different tasks, making it the first general-purpose across-domains classification model on graphs.

This work studies a central extremal graph theory problem inspired by a 1975 conjecture of Erdos, which aims to find graphs with a given size (number of nodes) that maximize the number of edges without having 3- or 4-cycles. We formulate this problem as a sequential decision-making problem and compare AlphaZero, a neural network-guided tree search, with tabu search, a heuristic local search method. Using either method, by introducing a curriculum -- jump-starting the search for larger graphs using good graphs found at smaller sizes -- we improve the state-of-the-art lower bounds for several sizes. We also propose a flexible graph-generation environment and a permutation-invariant network architecture for learning to search in the space of graphs.

Recently, there has been a surge of interest in employing neural networks for graph generation, a fundamental statistical learning problem with critical applications like molecule design and community analysis. However, most approaches encounter significant limitations when generating large-scale graphs. This is due to their requirement to output the full adjacency matrices whose size grows quadratically with the number of nodes. In response to this challenge, we introduce a new, simple, and scalable graph representation named gap encoded edge list (GEEL) that has a small representation size that aligns with the number of edges. In addition, GEEL significantly reduces the vocabulary size by incorporating the gap encoding and bandwidth restriction schemes. GEEL can be autoregressively generated with the incorporation of node positional encoding, and we further extend GEEL to deal with attributed graphs by designing a new grammar. Our findings reveal that the adoption of this compact representation not only enhances scalability but also bolsters performance by simplifying the graph generation process. We conduct a comprehensive evaluation across ten non-attributed and two molecular graph generation tasks, demonstrating the effectiveness of GEEL.

Graph Structure Learning (GSL) focuses on capturing intrinsic dependencies and interactions among nodes in graph-structured data by generating novel graph structures. Graph Neural Networks (GNNs) have emerged as promising GSL solutions, utilizing recursive message passing to encode node-wise inter-dependencies. However, many existing GSL methods heavily depend on explicit graph structural information as supervision signals, leaving them susceptible to challenges such as data noise and sparsity. In this work, we propose GraphEdit, an approach that leverages large language models (LLMs) to learn complex node relationships in graph-structured data. By enhancing the reasoning capabilities of LLMs through instruction-tuning over graph structures, we aim to overcome the limitations associated with explicit graph structural information and enhance the reliability of graph structure learning. Our approach not only effectively denoises noisy connections but also identifies node-wise dependencies from a global perspective, providing a comprehensive understanding of the graph structure. We conduct extensive experiments on multiple benchmark datasets to demonstrate the effectiveness and robustness of GraphEdit across various settings. We have made our model implementation available at: https://github.com/HKUDS/GraphEdit.

Graph mining workloads aim to extract structural properties of a graph by exploring its subgraph structures. General purpose graph mining systems provide a generic runtime to explore subgraph structures of interest with the help of user-defined functions that guide the overall exploration process. However, the state-of-the-art graph mining systems remain largely oblivious to the shape (or pattern) of the subgraphs that they mine. This causes them to: (a) explore unnecessary subgraphs; (b) perform expensive computations on the explored subgraphs; and, (c) hold intermediate partial subgraphs in memory; all of which affect their overall performance. Furthermore, their programming models are often tied to their underlying exploration strategies, which makes it difficult for domain users to express complex mining tasks. In this paper, we develop Peregrine, a pattern-aware graph mining system that directly explores the subgraphs of interest while avoiding exploration of unnecessary subgraphs, and simultaneously bypassing expensive computations throughout the mining process. We design a pattern-based programming model that treats "graph patterns" as first class constructs and enables Peregrine to extract the semantics of patterns, which it uses to guide its exploration. Our evaluation shows that Peregrine outperforms state-of-the-art distributed and single machine graph mining systems, and scales to complex mining tasks on larger graphs, while retaining simplicity and expressivity with its "pattern-first" programming approach.

Evaluating and enhancing the general capabilities of large language models (LLMs) has been an important research topic. Graph is a common data structure in the real world, and understanding graph data is a crucial part for advancing general intelligence. To evaluate and enhance the graph understanding abilities of LLMs, in this paper, we propose a benchmark named GraphInstruct, which comprehensively includes 21 classical graph reasoning tasks, providing diverse graph generation pipelines and detailed reasoning steps. Based on GraphInstruct, we further construct GraphLM through efficient instruction-tuning, which shows prominent graph understanding capability. In order to enhance the LLM with graph reasoning capability as well, we propose a step mask training strategy, and construct a model named GraphLM+. As one of the pioneering efforts to enhance the graph understanding and reasoning abilities of LLMs, extensive experiments have demonstrated the superiority of GraphLM and GraphLM+ over other LLMs. We look forward to more researchers exploring the potential of LLMs in the graph data mining domain through GraphInstruct. Our code for generating GraphInstruct is released publicly at: https://github.com/CGCL-codes/GraphInstruct.

Given a graph with textual attributes, we enable users to `chat with their graph': that is, to ask questions about the graph using a conversational interface. In response to a user's questions, our method provides textual replies and highlights the relevant parts of the graph. While existing works integrate large language models (LLMs) and graph neural networks (GNNs) in various ways, they mostly focus on either conventional graph tasks (such as node, edge, and graph classification), or on answering simple graph queries on small or synthetic graphs. In contrast, we develop a flexible question-answering framework targeting real-world textual graphs, applicable to multiple applications including scene graph understanding, common sense reasoning, and knowledge graph reasoning. Toward this goal, we first develop a Graph Question Answering (GraphQA) benchmark with data collected from different tasks. Then, we propose our G-Retriever method, introducing the first retrieval-augmented generation (RAG) approach for general textual graphs, which can be fine-tuned to enhance graph understanding via soft prompting. To resist hallucination and to allow for textual graphs that greatly exceed the LLM's context window size, G-Retriever performs RAG over a graph by formulating this task as a Prize-Collecting Steiner Tree optimization problem. Empirical evaluations show that our method outperforms baselines on textual graph tasks from multiple domains, scales well with larger graph sizes, and mitigates hallucination.~Our codes and datasets are available at: \url{https://github.com/XiaoxinHe/G-Retriever}

A subgraph is constructed by using a subset of vertices and edges of a given graph. There exist many graph properties that are hereditary for subgraphs. Hence, researchers from different communities have paid a great deal of attention in studying numerous subgraph problems, on top of the ordinary graph problems. Many algorithms are proposed in studying subgraph problems, where one common approach is by extracting the patterns and structures of a given graph. Due to the complex structures of certain types of graphs and to improve overall performances of the existing frameworks, machine learning techniques have recently been employed in dealing with various subgraph problems. In this article, we present a comprehensive review on five well known subgraph problems that have been tackled by using machine learning methods. They are subgraph isomorphism (both counting and matching), maximum common subgraph, community detection and community search problems. We provide an outline of each proposed method, and examine its designs and performances. We also explore non-learning-based algorithms for each problem and a brief discussion is given. We then suggest some promising research directions in this area, hoping that relevant subgraph problems can be tackled by using a similar strategy. Since there is a huge growth in employing machine learning techniques in recent years, we believe that this survey will serve as a good reference point to relevant research communities.

Graph learning has become indispensable for interpreting and harnessing relational data in diverse fields, ranging from recommendation systems to social network analysis. In this context, a variety of GNNs have emerged as promising methodologies for encoding the structural information of graphs. By effectively capturing the graph's underlying structure, these GNNs have shown great potential in enhancing performance in graph learning tasks, such as link prediction and node classification. However, despite their successes, a significant challenge persists: these advanced methods often face difficulties in generalizing to unseen graph data that significantly differs from the training instances. In this work, our aim is to advance the graph learning paradigm by developing a general graph foundation model. This model is designed to understand the complex topological patterns present in diverse graph data, enabling it to excel in zero-shot graph learning tasks across different downstream datasets. To achieve this goal, we address several key technical challenges in our OpenGraph model. Firstly, we propose a unified graph tokenizer to adapt our graph model to generalize well on unseen graph data, even when the underlying graph properties differ significantly from those encountered during training. Secondly, we develop a scalable graph transformer as the foundational encoder, which effectively captures node-wise dependencies within the global topological context. Thirdly, we introduce a data augmentation mechanism enhanced by a LLM to alleviate the limitations of data scarcity in real-world scenarios. Extensive experiments validate the effectiveness of our framework. By adapting our OpenGraph to new graph characteristics and comprehending the nuances of diverse graphs, our approach achieves remarkable zero-shot graph learning performance across various settings and domains.

Graphs are widely used for modeling relational data in real-world scenarios, such as social networks and urban computing. Existing LLM-based graph analysis approaches either integrate graph neural networks (GNNs) for specific machine learning tasks, limiting their transferability, or rely solely on LLMs' internal reasoning ability, resulting in suboptimal performance. To address these limitations, we take advantage of recent advances in LLM-based agents, which have shown capabilities of utilizing external knowledge or tools for problem solving. By simulating human problem-solving strategies such as analogy and collaboration, we propose a multi-agent system based on LLMs named GraphTeam, for graph analysis. GraphTeam consists of five LLM-based agents from three modules, and the agents with different specialities can collaborate with each other to address complex problems. Specifically, (1) input-output normalization module: the question agent extracts and refines four key arguments from the original question, facilitating the problem understanding, and the answer agent organizes the results to meet the output requirement; (2) external knowledge retrieval module: we first build a knowledge base consisting of relevant documentation and experience information, and then the search agent retrieves the most relevant entries for each question. (3) problem-solving module: given the retrieved information from search agent, the coding agent uses established algorithms via programming to generate solutions, and in case the coding agent does not work, the reasoning agent will directly compute the results without programming. Extensive experiments on six graph analysis benchmarks demonstrate that GraphTeam achieves state-of-the-art performance with an average 25.85% improvement over the best baseline in terms of accuracy. The code and data are available at https://github.com/BUPT-GAMMA/GraphTeam.

We present a new approach for the approximate K-nearest neighbor search based on navigable small world graphs with controllable hierarchy (Hierarchical NSW, HNSW). The proposed solution is fully graph-based, without any need for additional search structures, which are typically used at the coarse search stage of the most proximity graph techniques. Hierarchical NSW incrementally builds a multi-layer structure consisting from hierarchical set of proximity graphs (layers) for nested subsets of the stored elements. The maximum layer in which an element is present is selected randomly with an exponentially decaying probability distribution. This allows producing graphs similar to the previously studied Navigable Small World (NSW) structures while additionally having the links separated by their characteristic distance scales. Starting search from the upper layer together with utilizing the scale separation boosts the performance compared to NSW and allows a logarithmic complexity scaling. Additional employment of a heuristic for selecting proximity graph neighbors significantly increases performance at high recall and in case of highly clustered data. Performance evaluation has demonstrated that the proposed general metric space search index is able to strongly outperform previous opensource state-of-the-art vector-only approaches. Similarity of the algorithm to the skip list structure allows straightforward balanced distributed implementation.

Large Language Models (LLMs) have gained the ability to assimilate human knowledge and facilitate natural language interactions with both humans and other LLMs. However, despite their impressive achievements, LLMs have not made significant advancements in the realm of graph machine learning. This limitation arises because graphs encapsulate distinct relational data, making it challenging to transform them into natural language that LLMs understand. In this paper, we bridge this gap with a novel framework, GraphText, that translates graphs into natural language. GraphText derives a graph-syntax tree for each graph that encapsulates both the node attributes and inter-node relationships. Traversal of the tree yields a graph text sequence, which is then processed by an LLM to treat graph tasks as text generation tasks. Notably, GraphText offers multiple advantages. It introduces training-free graph reasoning: even without training on graph data, GraphText with ChatGPT can achieve on par with, or even surpassing, the performance of supervised-trained graph neural networks through in-context learning (ICL). Furthermore, GraphText paves the way for interactive graph reasoning, allowing both humans and LLMs to communicate with the model seamlessly using natural language. These capabilities underscore the vast, yet-to-be-explored potential of LLMs in the domain of graph machine learning.

Program source code contains complex structure information, which can be represented in structured data forms like trees or graphs. To acquire the structural information in source code, most existing researches use abstract syntax trees (AST). A group of works add additional edges to ASTs to convert source code into graphs and use graph neural networks to learn representations for program graphs. Although these works provide additional control or data flow information to ASTs for downstream tasks, they neglect an important aspect of structure information in AST itself: the different types of nodes and edges. In ASTs, different nodes contain different kinds of information like variables or control flow, and the relation between a node and all its children can also be different. To address the information of node and edge types, we bring the idea of heterogeneous graphs to learning on source code and present a new formula of building heterogeneous program graphs from ASTs with additional type information for nodes and edges. We use the ASDL grammar of programming language to define the node and edge types of program graphs. Then we use heterogeneous graph neural networks to learn on these graphs. We evaluate our approach on two tasks: code comment generation and method naming. Both tasks require reasoning on the semantics of complete code snippets. Experiment results show that our approach outperforms baseline models, including homogeneous graph-based models, showing that leveraging the type information of nodes and edges in program graphs can help in learning program semantics.

Large language models (LLMs) such as GPT-4 have emerged as frontrunners, showcasing unparalleled prowess in diverse applications, including answering queries, code generation, and more. Parallelly, graph-structured data, an intrinsic data type, is pervasive in real-world scenarios. Merging the capabilities of LLMs with graph-structured data has been a topic of keen interest. This paper bifurcates such integrations into two predominant categories. The first leverages LLMs for graph learning, where LLMs can not only augment existing graph algorithms but also stand as prediction models for various graph tasks. Conversely, the second category underscores the pivotal role of graphs in advancing LLMs. Mirroring human cognition, we solve complex tasks by adopting graphs in either reasoning or collaboration. Integrating with such structures can significantly boost the performance of LLMs in various complicated tasks. We also discuss and propose open questions for integrating LLMs with graph-structured data for the future direction of the field.

Large language models (LLMs) are increasingly adopted for a variety of tasks with implicit graphical structures, such as planning in robotics, multi-hop question answering or knowledge probing, structured commonsense reasoning, and more. While LLMs have advanced the state-of-the-art on these tasks with structure implications, whether LLMs could explicitly process textual descriptions of graphs and structures, map them to grounded conceptual spaces, and perform structured operations remains underexplored. To this end, we propose NLGraph (Natural Language Graph), a comprehensive benchmark of graph-based problem solving designed in natural language. NLGraph contains 29,370 problems, covering eight graph reasoning tasks with varying complexity from simple tasks such as connectivity and shortest path up to complex problems such as maximum flow and simulating graph neural networks. We evaluate LLMs (GPT-3/4) with various prompting approaches on the NLGraph benchmark and find that 1) language models do demonstrate preliminary graph reasoning abilities, 2) the benefit of advanced prompting and in-context learning diminishes on more complex graph problems, while 3) LLMs are also (un)surprisingly brittle in the face of spurious correlations in graph and problem settings. We then propose Build-a-Graph Prompting and Algorithmic Prompting, two instruction-based approaches to enhance LLMs in solving natural language graph problems. Build-a-Graph and Algorithmic prompting improve the performance of LLMs on NLGraph by 3.07% to 16.85% across multiple tasks and settings, while how to solve the most complicated graph reasoning tasks in our setup with language models remains an open research question. The NLGraph benchmark and evaluation code are available at https://github.com/Arthur-Heng/NLGraph.

Pre-trained sequence-to-sequence language models have led to widespread success in many natural language generation tasks. However, there has been relatively less work on analyzing their ability to generate structured outputs such as graphs. Unlike natural language, graphs have distinct structural and semantic properties in the context of a downstream NLP task, e.g., generating a graph that is connected and acyclic can be attributed to its structural constraints, while the semantics of a graph can refer to how meaningfully an edge represents the relation between two node concepts. In this work, we study pre-trained language models that generate explanation graphs in an end-to-end manner and analyze their ability to learn the structural constraints and semantics of such graphs. We first show that with limited supervision, pre-trained language models often generate graphs that either violate these constraints or are semantically incoherent. Since curating large amount of human-annotated graphs is expensive and tedious, we propose simple yet effective ways of graph perturbations via node and edge edit operations that lead to structurally and semantically positive and negative graphs. Next, we leverage these graphs in different contrastive learning models with Max-Margin and InfoNCE losses. Our methods lead to significant improvements in both structural and semantic accuracy of explanation graphs and also generalize to other similar graph generation tasks. Lastly, we show that human errors are the best negatives for contrastive learning and also that automatically generating more such human-like negative graphs can lead to further improvements. Our code and models are publicly available at https://github.com/swarnaHub/ExplagraphGen

Graph-structured data are the commonly used and have wide application scenarios in the real world. For these diverse applications, the vast variety of learning tasks, graph domains, and complex graph learning procedures present challenges for human experts when designing versatile graph learning approaches. Facing these challenges, large language models (LLMs) offer a potential solution due to the extensive knowledge and the human-like intelligence. This paper proposes a novel conceptual prototype for designing versatile graph learning methods with LLMs, with a particular focus on the "where" and "how" perspectives. From the "where" perspective, we summarize four key graph learning procedures, including task definition, graph data feature engineering, model selection and optimization, deployment and serving. We then explore the application scenarios of LLMs in these procedures across a wider spectrum. In the "how" perspective, we align the abilities of LLMs with the requirements of each procedure. Finally, we point out the promising directions that could better leverage the strength of LLMs towards versatile graph learning methods.

With the increasing number of new neural architecture designs and substantial existing neural architectures, it becomes difficult for the researchers to situate their contributions compared with existing neural architectures or establish the connections between their designs and other relevant ones. To discover similar neural architectures in an efficient and automatic manner, we define a new problem Neural Architecture Retrieval which retrieves a set of existing neural architectures which have similar designs to the query neural architecture. Existing graph pre-training strategies cannot address the computational graph in neural architectures due to the graph size and motifs. To fulfill this potential, we propose to divide the graph into motifs which are used to rebuild the macro graph to tackle these issues, and introduce multi-level contrastive learning to achieve accurate graph representation learning. Extensive evaluations on both human-designed and synthesized neural architectures demonstrate the superiority of our algorithm. Such a dataset which contains 12k real-world network architectures, as well as their embedding, is built for neural architecture retrieval.

Large Language Models (LLMs) have achieved impressive performance in text understanding and have become an essential tool for building smart assistants. Originally focusing on text, they have been enhanced with multimodal capabilities in recent works that successfully built visual instruction following assistants. As far as the graph modality goes, however, no such assistants have yet been developed. Graph structures are complex in that they represent relation between different features and are permutation invariant. Moreover, representing them in purely textual form does not always lead to good LLM performance even for finetuned models. As a result, there is a need to develop a new method to integrate graphs in LLMs for general graph understanding. This work explores the integration of the graph modality in LLM for general graph instruction following tasks. It aims at producing a deep learning model that enhances an underlying LLM with graph embeddings and trains it to understand them and to produce, given an instruction, an answer grounded in the graph representation. The approach performs significantly better than a graph to text approach and remains consistent even for larger graphs.

Graph pooling compresses graph information into a compact representation. State-of-the-art graph pooling methods follow a hierarchical approach, which reduces the graph size step-by-step. These methods must balance memory efficiency with preserving node information, depending on whether they use node dropping or node clustering. Additionally, fixed pooling ratios or numbers of pooling layers are predefined for all graphs, which prevents personalized pooling structures from being captured for each individual graph. In this work, inspired by bottom-up grammar induction, we propose an efficient graph parsing algorithm to infer the pooling structure, which then drives graph pooling. The resulting Graph Parsing Network (GPN) adaptively learns personalized pooling structure for each individual graph. GPN benefits from the discrete assignments generated by the graph parsing algorithm, allowing good memory efficiency while preserving node information intact. Experimental results on standard benchmarks demonstrate that GPN outperforms state-of-the-art graph pooling methods in graph classification tasks while being able to achieve competitive performance in node classification tasks. We also conduct a graph reconstruction task to show GPN's ability to preserve node information and measure both memory and time efficiency through relevant tests.

Graph generation is a critical task in numerous domains, including molecular design and social network analysis, due to its ability to model complex relationships and structured data. While most modern graph generative models utilize adjacency matrix representations, this work revisits an alternative approach that represents graphs as sequences of node set and edge set. We advocate for this approach due to its efficient encoding of graphs and propose a novel representation. Based on this representation, we introduce the Graph Generative Pre-trained Transformer (G2PT), an auto-regressive model that learns graph structures via next-token prediction. To further exploit G2PT's capabilities as a general-purpose foundation model, we explore fine-tuning strategies for two downstream applications: goal-oriented generation and graph property prediction. We conduct extensive experiments across multiple datasets. Results indicate that G2PT achieves superior generative performance on both generic graph and molecule datasets. Furthermore, G2PT exhibits strong adaptability and versatility in downstream tasks from molecular design to property prediction.

Hypergraphs are a powerful abstraction for representing higher-order interactions between entities of interest. To exploit these relationships in making downstream predictions, a variety of hypergraph neural network architectures have recently been proposed, in large part building upon precursors from the more traditional graph neural network (GNN) literature. Somewhat differently, in this paper we begin by presenting an expressive family of parameterized, hypergraph-regularized energy functions. We then demonstrate how minimizers of these energies effectively serve as node embeddings that, when paired with a parameterized classifier, can be trained end-to-end via a supervised bilevel optimization process. Later, we draw parallels between the implicit architecture of the predictive models emerging from the proposed bilevel hypergraph optimization, and existing GNN architectures in common use. Empirically, we demonstrate state-of-the-art results on various hypergraph node classification benchmarks. Code is available at https://github.com/yxzwang/PhenomNN.

Graphs or networks are a very convenient way to represent data with lots of interaction. Recently, Machine Learning on Graph data has gained a lot of traction. In particular, vertex classification and missing edge detection have very interesting applications, ranging from drug discovery to recommender systems. To achieve such tasks, tremendous work has been accomplished to learn embedding of nodes and edges into finite-dimension vector spaces. This task is called Graph Representation Learning. However, Graph Representation Learning techniques often display prohibitive time and memory complexities, preventing their use in real-time with business size graphs. In this paper, we address this issue by leveraging a degeneracy property of Graphs - the K-Core Decomposition. We present two techniques taking advantage of this decomposition to reduce the time and memory consumption of walk-based Graph Representation Learning algorithms. We evaluate the performances, expressed in terms of quality of embedding and computational resources, of the proposed techniques on several academic datasets. Our code is available at https://github.com/SBrandeis/kcore-embedding

Deep graph generative modeling has proven capable of learning the distribution of complex, multi-scale structures characterizing real-world graphs. However, one of the main limitations of existing methods is their large output space, which limits generation scalability and hinders accurate modeling of the underlying distribution. To overcome these limitations, we propose a novel approach that significantly reduces the output space of existing graph generative models. Specifically, starting from the observation that many real-world graphs have low graph bandwidth, we restrict graph bandwidth during training and generation. Our strategy improves both generation scalability and quality without increasing architectural complexity or reducing expressiveness. Our approach is compatible with existing graph generative methods, and we describe its application to both autoregressive and one-shot models. We extensively validate our strategy on synthetic and real datasets, including molecular graphs. Our experiments show that, in addition to improving generation efficiency, our approach consistently improves generation quality and reconstruction accuracy. The implementation is made available.

Recently, subgraph GNNs have emerged as an important direction for developing expressive graph neural networks (GNNs). While numerous architectures have been proposed, so far there is still a limited understanding of how various design paradigms differ in terms of expressive power, nor is it clear what design principle achieves maximal expressiveness with minimal architectural complexity. To address these fundamental questions, this paper conducts a systematic study of general node-based subgraph GNNs through the lens of Subgraph Weisfeiler-Lehman Tests (SWL). Our central result is to build a complete hierarchy of SWL with strictly growing expressivity. Concretely, we prove that any node-based subgraph GNN falls into one of the six SWL equivalence classes, among which SSWL achieves the maximal expressive power. We also study how these equivalence classes differ in terms of their practical expressiveness such as encoding graph distance and biconnectivity. Furthermore, we give a tight expressivity upper bound of all SWL algorithms by establishing a close relation with localized versions of WL and Folklore WL (FWL) tests. Our results provide insights into the power of existing subgraph GNNs, guide the design of new architectures, and point out their limitations by revealing an inherent gap with the 2-FWL test. Finally, experiments demonstrate that SSWL-inspired subgraph GNNs can significantly outperform prior architectures on multiple benchmarks despite great simplicity.

The arXiv has collected 1.5 million pre-print articles over 28 years, hosting literature from scientific fields including Physics, Mathematics, and Computer Science. Each pre-print features text, figures, authors, citations, categories, and other metadata. These rich, multi-modal features, combined with the natural graph structure---created by citation, affiliation, and co-authorship---makes the arXiv an exciting candidate for benchmarking next-generation models. Here we take the first necessary steps toward this goal, by providing a pipeline which standardizes and simplifies access to the arXiv's publicly available data. We use this pipeline to extract and analyze a 6.7 million edge citation graph, with an 11 billion word corpus of full-text research articles. We present some baseline classification results, and motivate application of more exciting generative graph models.

Low-dimensional embeddings of nodes in large graphs have proved extremely useful in a variety of prediction tasks, from content recommendation to identifying protein functions. However, most existing approaches require that all nodes in the graph are present during training of the embeddings; these previous approaches are inherently transductive and do not naturally generalize to unseen nodes. Here we present GraphSAGE, a general, inductive framework that leverages node feature information (e.g., text attributes) to efficiently generate node embeddings for previously unseen data. Instead of training individual embeddings for each node, we learn a function that generates embeddings by sampling and aggregating features from a node's local neighborhood. Our algorithm outperforms strong baselines on three inductive node-classification benchmarks: we classify the category of unseen nodes in evolving information graphs based on citation and Reddit post data, and we show that our algorithm generalizes to completely unseen graphs using a multi-graph dataset of protein-protein interactions.

Large language models (LLMs), while exhibiting exceptional performance, suffer from hallucinations, especially on knowledge-intensive tasks. Existing works propose to augment LLMs with individual text units retrieved from external knowledge corpora to alleviate the issue. However, in many domains, texts are interconnected (e.g., academic papers in a bibliographic graph are linked by citations and co-authorships) which form a (text-attributed) graph. The knowledge in such graphs is encoded not only in single texts/nodes but also in their associated connections. To facilitate the research of augmenting LLMs with graphs, we manually construct a Graph Reasoning Benchmark dataset called GRBench, containing 1,740 questions that can be answered with the knowledge from 10 domain graphs. Then, we propose a simple and effective framework called Graph Chain-of-thought (Graph-CoT) to augment LLMs with graphs by encouraging LLMs to reason on the graph iteratively. Each Graph-CoT iteration consists of three sub-steps: LLM reasoning, LLM-graph interaction, and graph execution. We conduct systematic experiments with three LLM backbones on GRBench, where Graph-CoT outperforms the baselines consistently. The code is available at https://github.com/PeterGriffinJin/Graph-CoT.

In this paper, we aim to develop a large language model (LLM) with the reasoning ability on complex graph data. Currently, LLMs have achieved very impressive performance on various natural language learning tasks, extensions of which have also been applied to study the vision tasks with multi-modal data. However, when it comes to the graph learning tasks, existing LLMs present very serious flaws due to their several inherited weaknesses in performing {multi-step logic reasoning}, {precise mathematical calculation} and {perception about the spatial and temporal factors}. To address such challenges, in this paper, we will investigate the principles, methodologies and algorithms to empower existing LLMs with graph reasoning ability, which will have tremendous impacts on the current research of both LLMs and graph learning. Inspired by the latest ChatGPT and Toolformer models, we propose the Graph-ToolFormer (Graph Reasoning oriented Toolformer) framework to teach LLMs themselves with prompts augmented by ChatGPT to use external graph reasoning API tools. Specifically, we will investigate to teach Graph-ToolFormer to handle various graph data reasoning tasks in this paper, including both (1) very basic graph data loading and graph property reasoning tasks, ranging from simple graph order and size to the graph diameter and periphery, and (2) more advanced reasoning tasks on real-world graph data, such as bibliographic networks, protein molecules, sequential recommender systems, social networks and knowledge graphs.

For a broad range of research, governmental and commercial applications it is important to understand the allegiances, communities and structure of key players in society. One promising direction towards extracting this information is to exploit the rich relational data in digital social networks (the social graph). As social media data sets are very large, most approaches make use of distributed computing systems for this purpose. Distributing graph processing requires solving many difficult engineering problems, which has lead some researchers to look at single-machine solutions that are faster and easier to maintain. In this article, we present a single-machine real-time system for large-scale graph processing that allows analysts to interactively explore graph structures. The key idea is that the aggregate actions of large numbers of users can be compressed into a data structure that encapsulates user similarities while being robust to noise and queryable in real-time. We achieve single machine real-time performance by compressing the neighbourhood of each vertex using minhash signatures and facilitate rapid queries through Locality Sensitive Hashing. These techniques reduce query times from hours using industrial desktop machines operating on the full graph to milliseconds on standard laptops. Our method allows exploration of strongly associated regions (i.e. communities) of large graphs in real-time on a laptop. It has been deployed in software that is actively used by social network analysts and offers another channel for media owners to monetise their data, helping them to continue to provide free services that are valued by billions of people globally.

Aiming at better representing multivariate relationships, this paper investigates a motif dimensional framework for higher-order graph learning. The graph learning effectiveness can be improved through OFFER. The proposed framework mainly aims at accelerating and improving higher-order graph learning results. We apply the acceleration procedure from the dimensional of network motifs. Specifically, the refined degree for nodes and edges are conducted in two stages: (1) employ motif degree of nodes to refine the adjacency matrix of the network; and (2) employ motif degree of edges to refine the transition probability matrix in the learning process. In order to assess the efficiency of the proposed framework, four popular network representation algorithms are modified and examined. By evaluating the performance of OFFER, both link prediction results and clustering results demonstrate that the graph representation learning algorithms enhanced with OFFER consistently outperform the original algorithms with higher efficiency.

Leveraging generative Artificial Intelligence (AI), we have transformed a dataset comprising 1,000 scientific papers into an ontological knowledge graph. Through an in-depth structural analysis, we have calculated node degrees, identified communities and connectivities, and evaluated clustering coefficients and betweenness centrality of pivotal nodes, uncovering fascinating knowledge architectures. The graph has an inherently scale-free nature, is highly connected, and can be used for graph reasoning by taking advantage of transitive and isomorphic properties that reveal unprecedented interdisciplinary relationships that can be used to answer queries, identify gaps in knowledge, propose never-before-seen material designs, and predict material behaviors. We compute deep node embeddings for combinatorial node similarity ranking for use in a path sampling strategy links dissimilar concepts that have previously not been related. One comparison revealed structural parallels between biological materials and Beethoven's 9th Symphony, highlighting shared patterns of complexity through isomorphic mapping. In another example, the algorithm proposed a hierarchical mycelium-based composite based on integrating path sampling with principles extracted from Kandinsky's 'Composition VII' painting. The resulting material integrates an innovative set of concepts that include a balance of chaos/order, adjustable porosity, mechanical strength, and complex patterned chemical functionalization. We uncover other isomorphisms across science, technology and art, revealing a nuanced ontology of immanence that reveal a context-dependent heterarchical interplay of constituents. Graph-based generative AI achieves a far higher degree of novelty, explorative capacity, and technical detail, than conventional approaches and establishes a widely useful framework for innovation by revealing hidden connections.

This paper studies the problem of embedding very large information networks into low-dimensional vector spaces, which is useful in many tasks such as visualization, node classification, and link prediction. Most existing graph embedding methods do not scale for real world information networks which usually contain millions of nodes. In this paper, we propose a novel network embedding method called the "LINE," which is suitable for arbitrary types of information networks: undirected, directed, and/or weighted. The method optimizes a carefully designed objective function that preserves both the local and global network structures. An edge-sampling algorithm is proposed that addresses the limitation of the classical stochastic gradient descent and improves both the effectiveness and the efficiency of the inference. Empirical experiments prove the effectiveness of the LINE on a variety of real-world information networks, including language networks, social networks, and citation networks. The algorithm is very efficient, which is able to learn the embedding of a network with millions of vertices and billions of edges in a few hours on a typical single machine. The source code of the LINE is available online.

Graph generation with Machine Learning is an open problem with applications in various research fields. In this work, we propose to cast the generative process of a graph into a sequential one, relying on a node ordering procedure. We use this sequential process to design a novel generative model composed of two recurrent neural networks that learn to predict the edges of graphs: the first network generates one endpoint of each edge, while the second network generates the other endpoint conditioned on the state of the first. We test our approach extensively on five different datasets, comparing with two well-known baselines coming from graph literature, and two recurrent approaches, one of which holds state of the art performances. Evaluation is conducted considering quantitative and qualitative characteristics of the generated samples. Results show that our approach is able to yield novel, and unique graphs originating from very different distributions, while retaining structural properties very similar to those in the training sample. Under the proposed evaluation framework, our approach is able to reach performances comparable to the current state of the art on the graph generation task.

Large language models (LLMs), such as ChatGPT and LLaMA, are creating significant advancements in natural language processing, due to their strong text encoding/decoding ability and newly found emergent capability (e.g., reasoning). While LLMs are mainly designed to process pure texts, there are many real-world scenarios where text data are associated with rich structure information in the form of graphs (e.g., academic networks, and e-commerce networks) or scenarios where graph data are paired with rich textual information (e.g., molecules with descriptions). Besides, although LLMs have shown their pure text-based reasoning ability, it is underexplored whether such ability can be generalized to graph scenarios (i.e., graph-based reasoning). In this paper, we provide a systematic review of scenarios and techniques related to large language models on graphs. We first summarize potential scenarios of adopting LLMs on graphs into three categories, namely pure graphs, text-rich graphs, and text-paired graphs. We then discuss detailed techniques for utilizing LLMs on graphs, including LLM as Predictor, LLM as Encoder, and LLM as Aligner, and compare the advantages and disadvantages of different schools of models. Furthermore, we mention the real-world applications of such methods and summarize open-source codes and benchmark datasets. Finally, we conclude with potential future research directions in this fast-growing field. The related source can be found at https://github.com/PeterGriffinJin/Awesome-Language-Model-on-Graphs.

Human knowledge provides a formal understanding of the world. Knowledge graphs that represent structural relations between entities have become an increasingly popular research direction towards cognition and human-level intelligence. In this survey, we provide a comprehensive review of knowledge graph covering overall research topics about 1) knowledge graph representation learning, 2) knowledge acquisition and completion, 3) temporal knowledge graph, and 4) knowledge-aware applications, and summarize recent breakthroughs and perspective directions to facilitate future research. We propose a full-view categorization and new taxonomies on these topics. Knowledge graph embedding is organized from four aspects of representation space, scoring function, encoding models, and auxiliary information. For knowledge acquisition, especially knowledge graph completion, embedding methods, path inference, and logical rule reasoning, are reviewed. We further explore several emerging topics, including meta relational learning, commonsense reasoning, and temporal knowledge graphs. To facilitate future research on knowledge graphs, we also provide a curated collection of datasets and open-source libraries on different tasks. In the end, we have a thorough outlook on several promising research directions.

Since the pioneering work on the lottery ticket hypothesis for graph neural networks (GNNs) was proposed in Chen et al. (2021), the study on finding graph lottery tickets (GLT) has become one of the pivotal focus in the GNN community, inspiring researchers to discover sparser GLT while achieving comparable performance to original dense networks. In parallel, the graph structure has gained substantial attention as a crucial factor in GNN training dynamics, also elucidated by several recent studies. Despite this, contemporary studies on GLT, in general, have not fully exploited inherent pathways in the graph structure and identified tickets in an iterative manner, which is time-consuming and inefficient. To address these limitations, we introduce TEDDY, a one-shot edge sparsification framework that leverages structural information by incorporating edge-degree information. Following edge sparsification, we encourage the parameter sparsity during training via simple projected gradient descent on the ell_0 ball. Given the target sparsity levels for both the graph structure and the model parameters, our TEDDY facilitates efficient and rapid realization of GLT within a single training. Remarkably, our experimental results demonstrate that TEDDY significantly surpasses conventional iterative approaches in generalization, even when conducting one-shot sparsification that solely utilizes graph structures, without taking feature information into account.

Machine learning on graphs has been extensively studied in both academic and industry. However, as the literature on graph learning booms with a vast number of emerging methods and techniques, it becomes increasingly difficult to manually design the optimal machine learning algorithm for different graph-related tasks. To solve this critical challenge, automated machine learning (AutoML) on graphs which combines the strength of graph machine learning and AutoML together, is gaining attention from the research community. Therefore, we comprehensively survey AutoML on graphs in this paper, primarily focusing on hyper-parameter optimization (HPO) and neural architecture search (NAS) for graph machine learning. We further overview libraries related to automated graph machine learning and in-depth discuss AutoGL, the first dedicated open-source library for AutoML on graphs. In the end, we share our insights on future research directions for automated graph machine learning. This paper is the first systematic and comprehensive review of automated machine learning on graphs to the best of our knowledge.

The advancement of Large Language Models (LLMs) has remarkably pushed the boundaries towards artificial general intelligence (AGI), with their exceptional ability on understanding diverse types of information, including but not limited to images and audio. Despite this progress, a critical gap remains in empowering LLMs to proficiently understand and reason on graph data. Recent studies underscore LLMs' underwhelming performance on fundamental graph reasoning tasks. In this paper, we endeavor to unearth the obstacles that impede LLMs in graph reasoning, pinpointing the common practice of converting graphs into natural language descriptions (Graph2Text) as a fundamental bottleneck. To overcome this impediment, we introduce GraphLLM, a pioneering end-to-end approach that synergistically integrates graph learning models with LLMs. This synergy equips LLMs with the ability to proficiently interpret and reason on graph data, harnessing the superior expressive power of graph learning models. Our empirical evaluations across four fundamental graph reasoning tasks validate the effectiveness of GraphLLM. The results exhibit a substantial average accuracy enhancement of 54.44%, alongside a noteworthy context reduction of 96.45% across various graph reasoning tasks.

Graph measures that express closeness or distance between nodes can be employed for graph nodes clustering using metric clustering algorithms. There are numerous measures applicable to this task, and which one performs better is an open question. We study the performance of 25 graph measures on generated graphs with different parameters. While usually measure comparisons are limited to general measure ranking on a particular dataset, we aim to explore the performance of various measures depending on graph features. Using an LFR graph generator, we create a dataset of 11780 graphs covering the whole LFR parameter space. For each graph, we assess the quality of clustering with k-means algorithm for each considered measure. Based on this, we determine the best measure for each area of the parameter space. We find that the parameter space consists of distinct zones where one particular measure is the best. We analyze the geometry of the resulting zones and describe it with simple criteria. Given particular graph parameters, this allows us to recommend a particular measure to use for clustering.

Communication is a key bottleneck for distributed graph neural network (GNN) training. This paper proposes GNNPipe, a new approach that scales the distributed full-graph deep GNN training. Being the first to use layer-level model parallelism for GNN training, GNNPipe partitions GNN layers among GPUs, each device performs the computation for a disjoint subset of consecutive GNN layers on the whole graph. Compared to graph parallelism with each GPU handling a graph partition, GNNPipe reduces the communication volume by a factor of the number of GNN layers. GNNPipe overcomes the unique challenges for pipelined layer-level model parallelism on the whole graph by partitioning it into dependent chunks, allowing the use of historical vertex embeddings, and applying specific training techniques to ensure convergence. We also propose a hybrid approach by combining GNNPipe with graph parallelism to handle large graphs, achieve better computer resource utilization and ensure model convergence. We build a general GNN training system supporting all three parallelism setting. Extensive experiments show that our method reduces the per-epoch training time by up to 2.45x (on average 1.58x) and reduces the communication volume and overhead by up to 22.89x and 27.21x (on average 8.69x and 11.60x), respectively, while achieving a comparable level of model accuracy and convergence speed compared to graph parallelism.

Embodied AI agents that search for objects in large environments such as households often need to make efficient decisions by predicting object locations based on partial information. We pose this as a new type of link prediction problem: link prediction on partially observable dynamic graphs. Our graph is a representation of a scene in which rooms and objects are nodes, and their relationships are encoded in the edges; only parts of the changing graph are known to the agent at each timestep. This partial observability poses a challenge to existing link prediction approaches, which we address. We propose a novel state representation -- Scene Graph Memory (SGM) -- with captures the agent's accumulated set of observations, as well as a neural net architecture called a Node Edge Predictor (NEP) that extracts information from the SGM to search efficiently. We evaluate our method in the Dynamic House Simulator, a new benchmark that creates diverse dynamic graphs following the semantic patterns typically seen at homes, and show that NEP can be trained to predict the locations of objects in a variety of environments with diverse object movement dynamics, outperforming baselines both in terms of new scene adaptability and overall accuracy. The codebase and more can be found at https://www.scenegraphmemory.com.

Semi-supervised learning (SSL) tackles the label missing problem by enabling the effective usage of unlabeled data. While existing SSL methods focus on the traditional setting, a practical and challenging scenario called label Missing Not At Random (MNAR) is usually ignored. In MNAR, the labeled and unlabeled data fall into different class distributions resulting in biased label imputation, which deteriorates the performance of SSL models. In this work, class transition tracking based Pseudo-Rectifying Guidance (PRG) is devised for MNAR. We explore the class-level guidance information obtained by the Markov random walk, which is modeled on a dynamically created graph built over the class tracking matrix. PRG unifies the historical information of class distribution and class transitions caused by the pseudo-rectifying procedure to maintain the model's unbiased enthusiasm towards assigning pseudo-labels to all classes, so as the quality of pseudo-labels on both popular classes and rare classes in MNAR could be improved. Finally, we show the superior performance of PRG across a variety of MNAR scenarios, outperforming the latest SSL approaches combining bias removal solutions by a large margin. Code and model weights are available at https://github.com/NJUyued/PRG4SSL-MNAR.

We propose a method that leverages graph neural networks, multi-level message passing, and unsupervised training to enable real-time prediction of realistic clothing dynamics. Whereas existing methods based on linear blend skinning must be trained for specific garments, our method is agnostic to body shape and applies to tight-fitting garments as well as loose, free-flowing clothing. Our method furthermore handles changes in topology (e.g., garments with buttons or zippers) and material properties at inference time. As one key contribution, we propose a hierarchical message-passing scheme that efficiently propagates stiff stretching modes while preserving local detail. We empirically show that our method outperforms strong baselines quantitatively and that its results are perceived as more realistic than state-of-the-art methods.

Detecting and recovering out-of-vocabulary (OOV) words is always challenging for Automatic Speech Recognition (ASR) systems. Many existing methods focus on modeling OOV words by modifying acoustic and language models and integrating context words cleverly into models. To train such complex models, we need a large amount of data with context words, additional training time, and increased model size. However, after getting the ASR transcription to recover context-based OOV words, the post-processing method has not been explored much. In this work, we propose a post-processing technique to improve the performance of context-based OOV recovery. We created an acoustically boosted language model with a sub-graph made at phone level with an OOV words list. We proposed two methods to determine a suitable cost function to retrieve the OOV words based on the context. The cost function is defined based on phonetic and acoustic knowledge for matching and recovering the correct context words in the decode. The effectiveness of the proposed cost function is evaluated at both word-level and sentence-level. The evaluation results show that this approach can recover an average of 50% context-based OOV words across multiple categories.

Counterfactual reasoning is widely recognized as one of the most challenging and intricate aspects of causality in artificial intelligence. In this paper, we evaluate the performance of large language models (LLMs) in counterfactual reasoning. In contrast to previous studies that primarily focus on commonsense causal reasoning, where LLMs often rely on prior knowledge for inference, we specifically assess their ability to perform counterfactual inference using a set of formal rules. To support this evaluation, we introduce a new benchmark dataset, CounterBench, comprising 1K counterfactual reasoning questions. The dataset is designed with varying levels of difficulty, diverse causal graph structures, distinct types of counterfactual questions, and multiple nonsensical name variants. Our experiments demonstrate that counterfactual reasoning poses a significant challenge for LLMs, with most models performing at levels comparable to random guessing. To enhance LLM's counterfactual reasoning ability, we propose a novel reasoning paradigm, CoIn, which guides LLMs through iterative reasoning and backtracking to systematically explore counterfactual solutions. Experimental results show that our method significantly improves LLM performance on counterfactual reasoning tasks and consistently enhances performance across different LLMs.Our dataset is available at https://huggingface.co/datasets/CounterBench/CounterBench.

Graph Neural Networks (GNNs) have advanced graph structure understanding via recursive information exchange and aggregation among graph nodes. To improve model robustness, self-supervised learning (SSL) has emerged as a promising approach for data augmentation. However, existing methods for generating pre-trained graph embeddings often rely on fine-tuning with specific downstream task labels, which limits their usability in scenarios where labeled data is scarce or unavailable. To address this, our research focuses on advancing the generalization capabilities of graph models in challenging zero-shot learning scenarios. Inspired by the success of large language models (LLMs), we aim to develop a graph-oriented LLM that can achieve high generalization across diverse downstream datasets and tasks, even without any information available from the downstream graph data. In this work, we present the GraphGPT framework that aligns LLMs with graph structural knowledge with a graph instruction tuning paradigm. Our framework incorporates a text-graph grounding component to establish a connection between textual information and graph structures. Additionally, we propose a dual-stage instruction tuning paradigm, accompanied by a lightweight graph-text alignment projector. This paradigm explores self-supervised graph structural signals and task-specific graph instructions, to guide LLMs in understanding complex graph structures and improving their adaptability across different downstream tasks. Our framework is evaluated on supervised and zero-shot graph learning tasks, demonstrating superior generalization and outperforming state-of-the-art baselines.

We propose a recipe on how to build a general, powerful, scalable (GPS) graph Transformer with linear complexity and state-of-the-art results on a diverse set of benchmarks. Graph Transformers (GTs) have gained popularity in the field of graph representation learning with a variety of recent publications but they lack a common foundation about what constitutes a good positional or structural encoding, and what differentiates them. In this paper, we summarize the different types of encodings with a clearer definition and categorize them as being local, global or relative. The prior GTs are constrained to small graphs with a few hundred nodes, here we propose the first architecture with a complexity linear in the number of nodes and edges O(N+E) by decoupling the local real-edge aggregation from the fully-connected Transformer. We argue that this decoupling does not negatively affect the expressivity, with our architecture being a universal function approximator on graphs. Our GPS recipe consists of choosing 3 main ingredients: (i) positional/structural encoding, (ii) local message-passing mechanism, and (iii) global attention mechanism. We provide a modular framework GraphGPS that supports multiple types of encodings and that provides efficiency and scalability both in small and large graphs. We test our architecture on 16 benchmarks and show highly competitive results in all of them, show-casing the empirical benefits gained by the modularity and the combination of different strategies.

An elusive goal in navigation research is to build an intelligent agent that can understand multimodal instructions including natural language and image, and perform useful navigation. To achieve this, we study a widely useful category of navigation tasks we call Multimodal Instruction Navigation with demonstration Tours (MINT), in which the environment prior is provided through a previously recorded demonstration video. Recent advances in Vision Language Models (VLMs) have shown a promising path in achieving this goal as it demonstrates capabilities in perceiving and reasoning about multimodal inputs. However, VLMs are typically trained to predict textual output and it is an open research question about how to best utilize them in navigation. To solve MINT, we present Mobility VLA, a hierarchical Vision-Language-Action (VLA) navigation policy that combines the environment understanding and common sense reasoning power of long-context VLMs and a robust low-level navigation policy based on topological graphs. The high-level policy consists of a long-context VLM that takes the demonstration tour video and the multimodal user instruction as input to find the goal frame in the tour video. Next, a low-level policy uses the goal frame and an offline constructed topological graph to generate robot actions at every timestep. We evaluated Mobility VLA in a 836m^2 real world environment and show that Mobility VLA has a high end-to-end success rates on previously unsolved multimodal instructions such as "Where should I return this?" while holding a plastic bin.

A unique aspect of human visual understanding is the ability to flexibly interpret abstract concepts: acquiring lifted rules explaining what they symbolize, grounding them across familiar and unfamiliar contexts, and making predictions or reasoning about them. While off-the-shelf vision-language models excel at making literal interpretations of images (e.g., recognizing object categories such as tree branches), they still struggle to make sense of such visual abstractions (e.g., how an arrangement of tree branches may form the walls of a maze). To address this challenge, we introduce Deep Schema Grounding (DSG), a framework that leverages explicit structured representations of visual abstractions for grounding and reasoning. At the core of DSG are schemas--dependency graph descriptions of abstract concepts that decompose them into more primitive-level symbols. DSG uses large language models to extract schemas, then hierarchically grounds concrete to abstract components of the schema onto images with vision-language models. The grounded schema is used to augment visual abstraction understanding. We systematically evaluate DSG and different methods in reasoning on our new Visual Abstractions Dataset, which consists of diverse, real-world images of abstract concepts and corresponding question-answer pairs labeled by humans. We show that DSG significantly improves the abstract visual reasoning performance of vision-language models, and is a step toward human-aligned understanding of visual abstractions.

Advanced compiler technology is crucial for enabling machine learning applications to run on novel hardware, but traditional compilers fail to deliver performance, popular auto-tuners have long search times and expert-optimized libraries introduce unsustainable costs. To address this, we developed LoopTune, a deep reinforcement learning compiler that optimizes tensor computations in deep learning models for the CPU. LoopTune optimizes tensor traversal order while using the ultra-fast lightweight code generator LoopNest to perform hardware-specific optimizations. With a novel graph-based representation and action space, LoopTune speeds up LoopNest by 3.2x, generating an order of magnitude faster code than TVM, 2.8x faster than MetaSchedule, and 1.08x faster than AutoTVM, consistently performing at the level of the hand-tuned library Numpy. Moreover, LoopTune tunes code in order of seconds.

Enterprise data lakes often suffer from substantial amounts of duplicate and redundant data, with data volumes ranging from terabytes to petabytes. This leads to both increased storage costs and unnecessarily high maintenance costs for these datasets. In this work, we focus on identifying and reducing redundancy in enterprise data lakes by addressing the problem of 'dataset containment'. To the best of our knowledge, this is one of the first works that addresses table-level containment at a large scale. We propose R2D2: a three-step hierarchical pipeline that efficiently identifies almost all instances of containment by progressively reducing the search space in the data lake. It first builds (i) a schema containment graph, followed by (ii) statistical min-max pruning, and finally, (iii) content level pruning. We further propose minimizing the total storage and access costs by optimally identifying redundant datasets that can be deleted (and reconstructed on demand) while respecting latency constraints. We implement our system on Azure Databricks clusters using Apache Spark for enterprise data stored in ADLS Gen2, and on AWS clusters for open-source data. In contrast to existing modified baselines that are inaccurate or take several days to run, our pipeline can process an enterprise customer data lake at the TB scale in approximately 5 hours with high accuracy. We present theoretical results as well as extensive empirical validation on both enterprise (scale of TBs) and open-source datasets (scale of MBs - GBs), which showcase the effectiveness of our pipeline.

Combinatorial inverse problems in high energy physics span enormous algorithmic challenges. This work presents a new deep learning driven clustering algorithm that utilizes a space-time non-local trainable graph constructor, a graph neural network, and a set transformer. The model is trained with loss functions at the graph node, edge and object level, including contrastive learning and meta-supervision. The algorithm can be applied to problems such as charged particle tracking, calorimetry, pile-up discrimination, jet physics, and beyond. We showcase the effectiveness of this cutting-edge AI approach through particle tracking simulations. The code is available online.

In applications such as elderly care, dementia anti-wandering and pandemic control, it is important to ensure that people are within a predefined area for their safety and well-being. We propose GEM, a practical, semi-supervised Geofencing system with network EMbedding, which is based only on ambient radio frequency (RF) signals. GEM models measured RF signal records as a weighted bipartite graph. With access points on one side and signal records on the other, it is able to precisely capture the relationships between signal records. GEM then learns node embeddings from the graph via a novel bipartite network embedding algorithm called BiSAGE, based on a Bipartite graph neural network with a novel bi-level SAmple and aggreGatE mechanism and non-uniform neighborhood sampling. Using the learned embeddings, GEM finally builds a one-class classification model via an enhanced histogram-based algorithm for in-out detection, i.e., to detect whether the user is inside the area or not. This model also keeps on improving with newly collected signal records. We demonstrate through extensive experiments in diverse environments that GEM shows state-of-the-art performance with up to 34% improvement in F-score. BiSAGE in GEM leads to a 54% improvement in F-score, as compared to the one without BiSAGE.

A new prior is proposed for learning representations of high-level concepts of the kind we manipulate with language. This prior can be combined with other priors in order to help disentangling abstract factors from each other. It is inspired by cognitive neuroscience theories of consciousness, seen as a bottleneck through which just a few elements, after having been selected by attention from a broader pool, are then broadcast and condition further processing, both in perception and decision-making. The set of recently selected elements one becomes aware of is seen as forming a low-dimensional conscious state. This conscious state is combining the few concepts constituting a conscious thought, i.e., what one is immediately conscious of at a particular moment. We claim that this architectural and information-processing constraint corresponds to assumptions about the joint distribution between high-level concepts. To the extent that these assumptions are generally true (and the form of natural language seems consistent with them), they can form a useful prior for representation learning. A low-dimensional thought or conscious state is analogous to a sentence: it involves only a few variables and yet can make a statement with very high probability of being true. This is consistent with a joint distribution (over high-level concepts) which has the form of a sparse factor graph, i.e., where the dependencies captured by each factor of the factor graph involve only very few variables while creating a strong dip in the overall energy function. The consciousness prior also makes it natural to map conscious states to natural language utterances or to express classical AI knowledge in a form similar to facts and rules, albeit capturing uncertainty as well as efficient search mechanisms implemented by attention mechanisms.

Empathetic conversation is psychologically supposed to be the result of conscious alignment and interaction between the cognition and affection of empathy. However, existing empathetic dialogue models usually consider only the affective aspect or treat cognition and affection in isolation, which limits the capability of empathetic response generation. In this work, we propose the CASE model for empathetic dialogue generation. It first builds upon a commonsense cognition graph and an emotional concept graph and then aligns the user's cognition and affection at both the coarse-grained and fine-grained levels. Through automatic and manual evaluation, we demonstrate that CASE outperforms state-of-the-art baselines of empathetic dialogues and can generate more empathetic and informative responses.

Graph convolutional neural networks have recently shown great potential for the task of zero-shot learning. These models are highly sample efficient as related concepts in the graph structure share statistical strength allowing generalization to new classes when faced with a lack of data. However, multi-layer architectures, which are required to propagate knowledge to distant nodes in the graph, dilute the knowledge by performing extensive Laplacian smoothing at each layer and thereby consequently decrease performance. In order to still enjoy the benefit brought by the graph structure while preventing dilution of knowledge from distant nodes, we propose a Dense Graph Propagation (DGP) module with carefully designed direct links among distant nodes. DGP allows us to exploit the hierarchical graph structure of the knowledge graph through additional connections. These connections are added based on a node's relationship to its ancestors and descendants. A weighting scheme is further used to weigh their contribution depending on the distance to the node to improve information propagation in the graph. Combined with finetuning of the representations in a two-stage training approach our method outperforms state-of-the-art zero-shot learning approaches.

We introduce Functional Group-Aware Representations for Small Molecules (FARM), a novel foundation model designed to bridge the gap between SMILES, natural language, and molecular graphs. The key innovation of FARM lies in its functional group-aware tokenization, which incorporates functional group information directly into the representations. This strategic reduction in tokenization granularity in a way that is intentionally interfaced with key drivers of functional properties (i.e., functional groups) enhances the model's understanding of chemical language, expands the chemical lexicon, more effectively bridging SMILES and natural language, and ultimately advances the model's capacity to predict molecular properties. FARM also represents molecules from two perspectives: by using masked language modeling to capture atom-level features and by employing graph neural networks to encode the whole molecule topology. By leveraging contrastive learning, FARM aligns these two views of representations into a unified molecular embedding. We rigorously evaluate FARM on the MoleculeNet dataset, where it achieves state-of-the-art performance on 10 out of 12 tasks. These results highlight FARM's potential to improve molecular representation learning, with promising applications in drug discovery and pharmaceutical research.

Fake base stations (FBSes) pose a significant security threat by impersonating legitimate base stations (BSes). Though efforts have been made to defeat this threat, up to this day, the presence of FBSes and the multi-step attacks (MSAs) stemming from them can lead to unauthorized surveillance, interception of sensitive information, and disruption of network services. Therefore, detecting these malicious entities is crucial to ensure the security and reliability of cellular networks. Traditional detection methods often rely on additional hardware, rules, signal scanning, changing protocol specifications, or cryptographic mechanisms that have limitations and incur huge infrastructure costs. In this paper, we develop FBSDetector-an effective and efficient detection solution that can reliably detect FBSes and MSAs from layer-3 network traces using machine learning (ML) at the user equipment (UE) side. To develop FBSDetector, we create FBSAD and MSAD, the first-ever high-quality and large-scale datasets incorporating instances of FBSes and 21 MSAs. These datasets capture the network traces in different real-world cellular network scenarios (including mobility and different attacker capabilities) incorporating legitimate BSes and FBSes. Our novel ML framework, specifically designed to detect FBSes in a multi-level approach for packet classification using stateful LSTM with attention and trace level classification and MSAs using graph learning, can effectively detect FBSes with an accuracy of 96% and a false positive rate of 2.96%, and recognize MSAs with an accuracy of 86% and a false positive rate of 3.28%. We deploy FBSDetector as a real-world solution to protect end-users through a mobile app and validate it in real-world environments. Compared to the existing heuristic-based solutions that fail to detect FBSes, FBSDetector can detect FBSes in the wild in real-time.

In this study, we present a technique that spans multi-scale views (global scale -- meaning brain network-level and local scale -- examining each individual ROI that constitutes the network) applied to resting-state fMRI volumes. Deep learning based classification is utilized in understanding neurodegeneration. The novelty of the proposed approach lies in utilizing two extreme scales of analysis. One branch considers the entire network within graph-analysis framework. Concurrently, the second branch scrutinizes each ROI within a network independently, focusing on evolution of dynamics. For each subject, graph-based approach employs partial correlation to profile the subject in a single graph where each ROI is a node, providing insights into differences in levels of participation. In contrast, non-linear analysis employs recurrence plots to profile a subject as a multichannel 2D image, revealing distinctions in underlying dynamics. The proposed approach is employed for classification of a cohort of 50 healthy control (HC) and 50 Mild Cognitive Impairment (MCI), sourced from ADNI dataset. Results point to: (1) reduced activity in ROIs such as PCC in MCI (2) greater activity in occipital in MCI, which is not seen in HC (3) when analysed for dynamics, all ROIs in MCI show greater predictability in time-series.

Open Source Software (OSS) is forming the spines of technology infrastructures, attracting millions of talents to contribute. Notably, it is challenging and critical to consider both the developers' interests and the semantic features of the project code to recommend appropriate development tasks to OSS developers. In this paper, we formulate the novel problem of code recommendation, whose purpose is to predict the future contribution behaviors of developers given their interaction history, the semantic features of source code, and the hierarchical file structures of projects. Considering the complex interactions among multiple parties within the system, we propose CODER, a novel graph-based code recommendation framework for open source software developers. CODER jointly models microscopic user-code interactions and macroscopic user-project interactions via a heterogeneous graph and further bridges the two levels of information through aggregation on file-structure graphs that reflect the project hierarchy. Moreover, due to the lack of reliable benchmarks, we construct three large-scale datasets to facilitate future research in this direction. Extensive experiments show that our CODER framework achieves superior performance under various experimental settings, including intra-project, cross-project, and cold-start recommendation. We will release all the datasets, code, and utilities for data retrieval upon the acceptance of this work.

Graphs can model complex relationships between objects, enabling a myriad of Web applications such as online page/article classification and social recommendation. While graph neural networks(GNNs) have emerged as a powerful tool for graph representation learning, in an end-to-end supervised setting, their performance heavily rely on a large amount of task-specific supervision. To reduce labeling requirement, the "pre-train, fine-tune" and "pre-train, prompt" paradigms have become increasingly common. In particular, prompting is a popular alternative to fine-tuning in natural language processing, which is designed to narrow the gap between pre-training and downstream objectives in a task-specific manner. However, existing study of prompting on graphs is still limited, lacking a universal treatment to appeal to different downstream tasks. In this paper, we propose GraphPrompt, a novel pre-training and prompting framework on graphs. GraphPrompt not only unifies pre-training and downstream tasks into a common task template, but also employs a learnable prompt to assist a downstream task in locating the most relevant knowledge from the pre-train model in a task-specific manner. Finally, we conduct extensive experiments on five public datasets to evaluate and analyze GraphPrompt.

Parameter-efficient finetuning (PEFT) is a widely used technique to adapt large language models for different tasks. Service providers typically create separate systems for users to perform PEFT model finetuning and inference tasks. This is because existing systems cannot handle workloads that include a mix of inference and PEFT finetuning requests. As a result, shared GPU resources are underutilized, leading to inefficiencies. To address this problem, we present FlexLLM, the first system that can serve inference and parameter-efficient finetuning requests in the same iteration. Our system leverages the complementary nature of these two tasks and utilizes shared GPU resources to run them jointly, using a method called co-serving. To achieve this, FlexLLM introduces a novel token-level finetuning mechanism, which breaks down the finetuning computation of a sequence into smaller token-level computations and uses dependent parallelization and graph pruning, two static compilation optimizations, to minimize the memory overhead and latency for co-serving. Compared to existing systems, FlexLLM's co-serving approach reduces the activation GPU memory overhead by up to 8x, and the end-to-end GPU memory requirement of finetuning by up to 36% while maintaining a low inference latency and improving finetuning throughput. For example, under a heavy inference workload, FlexLLM can still preserve more than 80% of the peak finetuning throughput, whereas existing systems cannot make any progress with finetuning. The source code of FlexLLM is publicly available at https://github.com/flexflow/FlexFlow.

Search is an ability foundational in many important tasks, and recent studies have shown that large language models (LLMs) struggle to perform search robustly. It is unknown whether this inability is due to a lack of data, insufficient model parameters, or fundamental limitations of the transformer architecture. In this work, we use the foundational graph connectivity problem as a testbed to generate effectively limitless high-coverage data to train small transformers and test whether they can learn to perform search. We find that, when given the right training distribution, the transformer is able to learn to search. We analyze the algorithm that the transformer has learned through a novel mechanistic interpretability technique that enables us to extract the computation graph from the trained model. We find that for each vertex in the input graph, transformers compute the set of vertices reachable from that vertex. Each layer then progressively expands these sets, allowing the model to search over a number of vertices exponential in the number of layers. However, we find that as the input graph size increases, the transformer has greater difficulty in learning the task. This difficulty is not resolved even as the number of parameters is increased, suggesting that increasing model scale will not lead to robust search abilities. We also find that performing search in-context (i.e., chain-of-thought) does not resolve this inability to learn to search on larger graphs.

GraphRAG addresses significant challenges in Retrieval-Augmented Generation (RAG) by leveraging graphs with embedded knowledge to enhance the reasoning capabilities of Large Language Models (LLMs). Despite its promising potential, the GraphRAG community currently lacks a unified framework for fine-grained decomposition of the graph-based knowledge retrieval process. Furthermore, there is no systematic categorization or evaluation of existing solutions within the retrieval process. In this paper, we present LEGO-GraphRAG, a modular framework that decomposes the retrieval process of GraphRAG into three interconnected modules: subgraph-extraction, path-filtering, and path-refinement. We systematically summarize and classify the algorithms and neural network (NN) models relevant to each module, providing a clearer understanding of the design space for GraphRAG instances. Additionally, we identify key design factors, such as Graph Coupling and Computational Cost, that influence the effectiveness of GraphRAG implementations. Through extensive empirical studies, we construct high-quality GraphRAG instances using a representative selection of solutions and analyze their impact on retrieval and reasoning performance. Our findings offer critical insights into optimizing GraphRAG instance design, ultimately contributing to the advancement of more accurate and contextually relevant LLM applications.

Recent advances in large language models (LLMs) have increased the demand for comprehensive benchmarks to evaluate their capabilities as human-like agents. Existing benchmarks, while useful, often focus on specific application scenarios, emphasizing task completion but failing to dissect the underlying skills that drive these outcomes. This lack of granularity makes it difficult to deeply discern where failures stem from. Additionally, setting up these environments requires considerable effort, and issues of unreliability and reproducibility sometimes arise, especially in interactive tasks. To address these limitations, we introduce the Massive Multitask Agent Understanding (MMAU) benchmark, featuring comprehensive offline tasks that eliminate the need for complex environment setups. It evaluates models across five domains, including teal{Tool-use}, teal{Directed Acyclic Graph (DAG) QA}, teal{Data Science and Machine Learning coding}, teal{Contest-level programming} and teal{Mathematics}, and covers five essential capabilities: orange{Understanding}, orange{Reasoning}, orange{Planning}, orange{Problem-solving}, and orange{Self-correction}. With a total of 20 meticulously designed tasks encompassing over 3K distinct prompts, MMAU provides a comprehensive framework for evaluating the strengths and limitations of LLM agents. By testing 18 representative models on MMAU, we provide deep and insightful analyses. Ultimately, MMAU not only sheds light on the capabilities and limitations of LLM agents but also enhances the interpretability of their performance. Datasets and evaluation scripts of MMAU are released at https://github.com/apple/axlearn/docs/research/mmau.

We introduce NeuroSA, a neuromorphic architecture specifically designed to ensure asymptotic convergence to the ground state of an Ising problem using an annealing process that is governed by the physics of quantum mechanical tunneling using Fowler-Nordheim (FN). The core component of NeuroSA consists of a pair of asynchronous ON-OFF neurons, which effectively map classical simulated annealing (SA) dynamics onto a network of integrate-and-fire (IF) neurons. The threshold of each ON-OFF neuron pair is adaptively adjusted by an FN annealer which replicates the optimal escape mechanism and convergence of SA, particularly at low temperatures. To validate the effectiveness of our neuromorphic Ising machine, we systematically solved various benchmark MAX-CUT combinatorial optimization problems. Across multiple runs, NeuroSA consistently generates solutions that approach the state-of-the-art level with high accuracy (greater than 99%), and without any graph-specific hyperparameter tuning. For practical illustration, we present results from an implementation of NeuroSA on the SpiNNaker2 platform, highlighting the feasibility of mapping our proposed architecture onto a standard neuromorphic accelerator platform.

A booming amount of information is continuously added to the Internet as structured and unstructured data, feeding knowledge bases such as DBpedia and Wikidata with billions of statements describing millions of entities. The aim of Question Answering systems is to allow lay users to access such data using natural language without needing to write formal queries. However, users often submit questions that are complex and require a certain level of abstraction and reasoning to decompose them into basic graph patterns. In this short paper, we explore the use of architectures based on Neural Machine Translation called Neural SPARQL Machines to learn pattern compositions. We show that sequence-to-sequence models are a viable and promising option to transform long utterances into complex SPARQL queries.

While deep learning models have achieved state-of-the-art accuracies for many prediction tasks, understanding these models remains a challenge. Despite the recent interest in developing visual tools to help users interpret deep learning models, the complexity and wide variety of models deployed in industry, and the large-scale datasets that they used, pose unique design challenges that are inadequately addressed by existing work. Through participatory design sessions with over 15 researchers and engineers at Facebook, we have developed, deployed, and iteratively improved ActiVis, an interactive visualization system for interpreting large-scale deep learning models and results. By tightly integrating multiple coordinated views, such as a computation graph overview of the model architecture, and a neuron activation view for pattern discovery and comparison, users can explore complex deep neural network models at both the instance- and subset-level. ActiVis has been deployed on Facebook's machine learning platform. We present case studies with Facebook researchers and engineers, and usage scenarios of how ActiVis may work with different models.

We study a new connection between a technical measure called mu-conductance that arises in the study of Markov chains for sampling convex bodies and the network community profile that characterizes size-resolved properties of clusters and communities in social and information networks. The idea of mu-conductance is similar to the traditional graph conductance, but disregards sets with small volume. We derive a sequence of optimization problems including a low-rank semi-definite program from which we can derive a lower bound on the optimal mu-conductance value. These ideas give the first theoretically sound bound on the behavior of the network community profile for a wide range of cluster sizes. The algorithm scales up to graphs with hundreds of thousands of nodes and we demonstrate how our framework validates the predicted structures of real-world graphs.

We present RelBench, a public benchmark for solving predictive tasks over relational databases with graph neural networks. RelBench provides databases and tasks spanning diverse domains and scales, and is intended to be a foundational infrastructure for future research. We use RelBench to conduct the first comprehensive study of Relational Deep Learning (RDL) (Fey et al., 2024), which combines graph neural network predictive models with (deep) tabular models that extract initial entity-level representations from raw tables. End-to-end learned RDL models fully exploit the predictive signal encoded in primary-foreign key links, marking a significant shift away from the dominant paradigm of manual feature engineering combined with tabular models. To thoroughly evaluate RDL against this prior gold-standard, we conduct an in-depth user study where an experienced data scientist manually engineers features for each task. In this study, RDL learns better models whilst reducing human work needed by more than an order of magnitude. This demonstrates the power of deep learning for solving predictive tasks over relational databases, opening up many new research opportunities enabled by RelBench.

Ontologies and knowledge graphs (KGs) are general-purpose computable representations of some domain, such as human anatomy, and are frequently a crucial part of modern information systems. Most of these structures change over time, incorporating new knowledge or information that was previously missing. Managing these changes is a challenge, both in terms of communicating changes to users, and providing mechanisms to make it easier for multiple stakeholders to contribute. To fill that need, we have created KGCL, the Knowledge Graph Change Language, a standard data model for describing changes to KGs and ontologies at a high level, and an accompanying human-readable controlled natural language. This language serves two purposes: a curator can use it to request desired changes, and it can also be used to describe changes that have already happened, corresponding to the concepts of "apply patch" and "diff" commonly used for managing changes in text documents and computer programs. Another key feature of KGCL is that descriptions are at a high enough level to be useful and understood by a variety of stakeholders--for example, ontology edits can be specified by commands like "add synonym 'arm' to 'forelimb'" or "move 'Parkinson disease' under 'neurodegenerative disease'". We have also built a suite of tools for managing ontology changes. These include an automated agent that integrates with and monitors GitHub ontology repositories and applies any requested changes, and a new component in the BioPortal ontology resource that allows users to make change requests directly from within the BioPortal user interface. Overall, the KGCL data model, its controlled natural language, and associated tooling allow for easier management and processing of changes associated with the development of ontologies and KGs.

Recently, pre-trained foundation models have enabled significant advancements in multiple fields. In molecular machine learning, however, where datasets are often hand-curated, and hence typically small, the lack of datasets with labeled features, and codebases to manage those datasets, has hindered the development of foundation models. In this work, we present seven novel datasets categorized by size into three distinct categories: ToyMix, LargeMix and UltraLarge. These datasets push the boundaries in both the scale and the diversity of supervised labels for molecular learning. They cover nearly 100 million molecules and over 3000 sparsely defined tasks, totaling more than 13 billion individual labels of both quantum and biological nature. In comparison, our datasets contain 300 times more data points than the widely used OGB-LSC PCQM4Mv2 dataset, and 13 times more than the quantum-only QM1B dataset. In addition, to support the development of foundational models based on our proposed datasets, we present the Graphium graph machine learning library which simplifies the process of building and training molecular machine learning models for multi-task and multi-level molecular datasets. Finally, we present a range of baseline results as a starting point of multi-task and multi-level training on these datasets. Empirically, we observe that performance on low-resource biological datasets show improvement by also training on large amounts of quantum data. This indicates that there may be potential in multi-task and multi-level training of a foundation model and fine-tuning it to resource-constrained downstream tasks.

Binary silhouettes and keypoint-based skeletons have dominated human gait recognition studies for decades since they are easy to extract from video frames. Despite their success in gait recognition for in-the-lab environments, they usually fail in real-world scenarios due to their low information entropy for gait representations. To achieve accurate gait recognition in the wild, this paper presents a novel gait representation, named Gait Parsing Sequence (GPS). GPSs are sequences of fine-grained human segmentation, i.e., human parsing, extracted from video frames, so they have much higher information entropy to encode the shapes and dynamics of fine-grained human parts during walking. Moreover, to effectively explore the capability of the GPS representation, we propose a novel human parsing-based gait recognition framework, named ParsingGait. ParsingGait contains a Convolutional Neural Network (CNN)-based backbone and two light-weighted heads. The first head extracts global semantic features from GPSs, while the other one learns mutual information of part-level features through Graph Convolutional Networks to model the detailed dynamics of human walking. Furthermore, due to the lack of suitable datasets, we build the first parsing-based dataset for gait recognition in the wild, named Gait3D-Parsing, by extending the large-scale and challenging Gait3D dataset. Based on Gait3D-Parsing, we comprehensively evaluate our method and existing gait recognition methods. The experimental results show a significant improvement in accuracy brought by the GPS representation and the superiority of ParsingGait. The code and dataset are available at https://gait3d.github.io/gait3d-parsing-hp .

We extend conformal prediction to control the expected value of any monotone loss function. The algorithm generalizes split conformal prediction together with its coverage guarantee. Like conformal prediction, the conformal risk control procedure is tight up to an O(1/n) factor. We also introduce extensions of the idea to distribution shift, quantile risk control, multiple and adversarial risk control, and expectations of U-statistics. Worked examples from computer vision and natural language processing demonstrate the usage of our algorithm to bound the false negative rate, graph distance, and token-level F1-score.

We tackle real-world problems with complex structures beyond the pixel-based game or simulator. We formulate it as a few-shot reinforcement learning problem where a task is characterized by a subtask graph that defines a set of subtasks and their dependencies that are unknown to the agent. Different from the previous meta-rl methods trying to directly infer the unstructured task embedding, our multi-task subtask graph inferencer (MTSGI) first infers the common high-level task structure in terms of the subtask graph from the training tasks, and use it as a prior to improve the task inference in testing. Our experiment results on 2D grid-world and complex web navigation domains show that the proposed method can learn and leverage the common underlying structure of the tasks for faster adaptation to the unseen tasks than various existing algorithms such as meta reinforcement learning, hierarchical reinforcement learning, and other heuristic agents.

Document-level Relation Extraction (RE) is a more challenging task than sentence RE as it often requires reasoning over multiple sentences. Yet, human annotators usually use a small number of sentences to identify the relationship between a given entity pair. In this paper, we present an embarrassingly simple but effective method to heuristically select evidence sentences for document-level RE, which can be easily combined with BiLSTM to achieve good performance on benchmark datasets, even better than fancy graph neural network based methods. We have released our code at https://github.com/AndrewZhe/Three-Sentences-Are-All-You-Need.

Dynamics models learned from visual observations have shown to be effective in various robotic manipulation tasks. One of the key questions for learning such dynamics models is what scene representation to use. Prior works typically assume representation at a fixed dimension or resolution, which may be inefficient for simple tasks and ineffective for more complicated tasks. In this work, we investigate how to learn dynamic and adaptive representations at different levels of abstraction to achieve the optimal trade-off between efficiency and effectiveness. Specifically, we construct dynamic-resolution particle representations of the environment and learn a unified dynamics model using graph neural networks (GNNs) that allows continuous selection of the abstraction level. During test time, the agent can adaptively determine the optimal resolution at each model-predictive control (MPC) step. We evaluate our method in object pile manipulation, a task we commonly encounter in cooking, agriculture, manufacturing, and pharmaceutical applications. Through comprehensive evaluations both in the simulation and the real world, we show that our method achieves significantly better performance than state-of-the-art fixed-resolution baselines at the gathering, sorting, and redistribution of granular object piles made with various instances like coffee beans, almonds, corn, etc.

Current low-precision quantization algorithms often have the hidden cost of conversion back and forth from floating point to quantized integer values. This hidden cost limits the latency improvement realized by quantizing Neural Networks. To address this, we present HAWQV3, a novel mixed-precision integer-only quantization framework. The contributions of HAWQV3 are the following: (i) An integer-only inference where the entire computational graph is performed only with integer multiplication, addition, and bit shifting, without any floating point operations or even integer division; (ii) A novel hardware-aware mixed-precision quantization method where the bit-precision is calculated by solving an integer linear programming problem that balances the trade-off between model perturbation and other constraints, e.g., memory footprint and latency; (iii) Direct hardware deployment and open source contribution for 4-bit uniform/mixed-precision quantization in TVM, achieving an average speed up of 1.45times for uniform 4-bit, as compared to uniform 8-bit for ResNet50 on T4 GPUs; and (iv) extensive evaluation of the proposed methods on ResNet18/50 and InceptionV3, for various model compression levels with/without mixed precision. For ResNet50, our INT8 quantization achieves an accuracy of 77.58%, which is 2.68% higher than prior integer-only work, and our mixed-precision INT4/8 quantization can reduce INT8 latency by 23% and still achieve 76.73% accuracy. Our framework and the TVM implementation have been open sourced.

Which transformer scaling regimes are able to perfectly solve different classes of algorithmic problems? While tremendous empirical advances have been attained by transformer-based neural networks, a theoretical understanding of their algorithmic reasoning capabilities in realistic parameter regimes is lacking. We investigate this question in terms of the network's depth, width, and number of extra tokens for algorithm execution. Our novel representational hierarchy separates 9 algorithmic reasoning problems into classes solvable by transformers in different realistic parameter scaling regimes. We prove that logarithmic depth is necessary and sufficient for tasks like graph connectivity, while single-layer transformers with small embedding dimensions can solve contextual retrieval tasks. We also support our theoretical analysis with ample empirical evidence using the GraphQA benchmark. These results show that transformers excel at many graph reasoning tasks, even outperforming specialized graph neural networks.

Seminal research in the field of graph neural networks (GNNs) has revealed a direct correspondence between the expressive capabilities of GNNs and the k-dimensional Weisfeiler-Leman (kWL) test, a widely-recognized method for verifying graph isomorphism. This connection has reignited interest in comprehending the specific graph properties effectively distinguishable by the kWL test. A central focus of research in this field revolves around determining the least dimensionality k, for which kWL can discern graphs with different number of occurrences of a pattern graph P. We refer to such a least k as the WL-dimension of this pattern counting problem. This inquiry traditionally delves into two distinct counting problems related to patterns: subgraph counting and induced subgraph counting. Intriguingly, despite their initial appearance as separate challenges with seemingly divergent approaches, both of these problems are interconnected components of a more comprehensive problem: "graph motif parameters". In this paper, we provide a precise characterization of the WL-dimension of labeled graph motif parameters. As specific instances of this result, we obtain characterizations of the WL-dimension of the subgraph counting and induced subgraph counting problem for every labeled pattern P. We additionally demonstrate that in cases where the kWL test distinguishes between graphs with varying occurrences of a pattern P, the exact number of occurrences of P can be computed uniformly using only local information of the last layer of a corresponding GNN. We finally delve into the challenge of recognizing the WL-dimension of various graph parameters. We give a polynomial time algorithm for determining the WL-dimension of the subgraph counting problem for given pattern P, answering an open question from previous work.

We investigate the problem of producing structured graph representations of visual scenes. Our work analyzes the role of motifs: regularly appearing substructures in scene graphs. We present new quantitative insights on such repeated structures in the Visual Genome dataset. Our analysis shows that object labels are highly predictive of relation labels but not vice-versa. We also find that there are recurring patterns even in larger subgraphs: more than 50% of graphs contain motifs involving at least two relations. Our analysis motivates a new baseline: given object detections, predict the most frequent relation between object pairs with the given labels, as seen in the training set. This baseline improves on the previous state-of-the-art by an average of 3.6% relative improvement across evaluation settings. We then introduce Stacked Motif Networks, a new architecture designed to capture higher order motifs in scene graphs that further improves over our strong baseline by an average 7.1% relative gain. Our code is available at github.com/rowanz/neural-motifs.

Graph Neural Networks (GNNs) have shown great promise in learning node embeddings for link prediction (LP). While numerous studies aim to improve the overall LP performance of GNNs, none have explored its varying performance across different nodes and its underlying reasons. To this end, we aim to demystify which nodes will perform better from the perspective of their local topology. Despite the widespread belief that low-degree nodes exhibit poorer LP performance, our empirical findings provide nuances to this viewpoint and prompt us to propose a better metric, Topological Concentration (TC), based on the intersection of the local subgraph of each node with the ones of its neighbors. We empirically demonstrate that TC has a higher correlation with LP performance than other node-level topological metrics like degree and subgraph density, offering a better way to identify low-performing nodes than using cold-start. With TC, we discover a novel topological distribution shift issue in which newly joined neighbors of a node tend to become less interactive with that node's existing neighbors, compromising the generalizability of node embeddings for LP at testing time. To make the computation of TC scalable, We further propose Approximated Topological Concentration (ATC) and theoretically/empirically justify its efficacy in approximating TC and reducing the computation complexity. Given the positive correlation between node TC and its LP performance, we explore the potential of boosting LP performance via enhancing TC by re-weighting edges in the message-passing and discuss its effectiveness with limitations. Our code is publicly available at https://github.com/YuWVandy/Topo_LP_GNN.

Graph neural networks (GNNs) are a powerful architecture for tackling graph learning tasks, yet have been shown to be oblivious to eminent substructures such as cycles. We present TOGL, a novel layer that incorporates global topological information of a graph using persistent homology. TOGL can be easily integrated into any type of GNN and is strictly more expressive (in terms the Weisfeiler--Lehman graph isomorphism test) than message-passing GNNs. Augmenting GNNs with TOGL leads to improved predictive performance for graph and node classification tasks, both on synthetic data sets, which can be classified by humans using their topology but not by ordinary GNNs, and on real-world data.

We study the implications of the modeling choice to use a graph, instead of a hypergraph, to represent real-world interconnected systems whose constituent relationships are of higher order by nature. Such a modeling choice typically involves an underlying projection process that maps the original hypergraph onto a graph, and is common in graph-based analysis. While hypergraph projection can potentially lead to loss of higher-order relations, there exists very limited studies on the consequences of doing so, as well as its remediation. This work fills this gap by doing two things: (1) we develop analysis based on graph and set theory, showing two ubiquitous patterns of hyperedges that are root to structural information loss in all hypergraph projections; we also quantify the combinatorial impossibility of recovering the lost higher-order structures if no extra help is provided; (2) we still seek to recover the lost higher-order structures in hypergraph projection, and in light of (1)'s findings we propose to relax the problem into a learning-based setting. Under this setting, we develop a learning-based hypergraph reconstruction method based on an important statistic of hyperedge distributions that we find. Our reconstruction method is evaluated on 8 real-world datasets under different settings, and exhibits consistently good performance. We also demonstrate benefits of the reconstructed hypergraphs via use cases of protein rankings and link predictions.

Stepwise inference protocols, such as scratchpads and chain-of-thought, help language models solve complex problems by decomposing them into a sequence of simpler subproblems. Despite the significant gain in performance achieved via these protocols, the underlying mechanisms of stepwise inference have remained elusive. To address this, we propose to study autoregressive Transformer models on a synthetic task that embodies the multi-step nature of problems where stepwise inference is generally most useful. Specifically, we define a graph navigation problem wherein a model is tasked with traversing a path from a start to a goal node on the graph. Despite is simplicity, we find we can empirically reproduce and analyze several phenomena observed at scale: (i) the stepwise inference reasoning gap, the cause of which we find in the structure of the training data; (ii) a diversity-accuracy tradeoff in model generations as sampling temperature varies; (iii) a simplicity bias in the model's output; and (iv) compositional generalization and a primacy bias with in-context exemplars. Overall, our work introduces a grounded, synthetic framework for studying stepwise inference and offers mechanistic hypotheses that can lay the foundation for a deeper understanding of this phenomenon.

Existing graph matching methods typically assume that there are similar structures between graphs and they are matchable. However, these assumptions do not align with real-world applications. This work addresses a more realistic scenario where graphs exhibit diverse modes, requiring graph grouping before or along with matching, a task termed mixture graph matching and clustering. We introduce Minorize-Maximization Matching and Clustering (M3C), a learning-free algorithm that guarantees theoretical convergence through the Minorize-Maximization framework and offers enhanced flexibility via relaxed clustering. Building on M3C, we develop UM3C, an unsupervised model that incorporates novel edge-wise affinity learning and pseudo label selection. Extensive experimental results on public benchmarks demonstrate that our method outperforms state-of-the-art graph matching and mixture graph matching and clustering approaches in both accuracy and efficiency. Source code will be made publicly available.

Graph generation is integral to various engineering and scientific disciplines. Nevertheless, existing methodologies tend to overlook the generation of edge attributes. However, we identify critical applications where edge attributes are essential, making prior methods potentially unsuitable in such contexts. Moreover, while trivial adaptations are available, empirical investigations reveal their limited efficacy as they do not properly model the interplay among graph components. To address this, we propose a joint score-based model of nodes and edges for graph generation that considers all graph components. Our approach offers two key novelties: (i) node and edge attributes are combined in an attention module that generates samples based on the two ingredients; and (ii) node, edge and adjacency information are mutually dependent during the graph diffusion process. We evaluate our method on challenging benchmarks involving real-world and synthetic datasets in which edge features are crucial. Additionally, we introduce a new synthetic dataset that incorporates edge values. Furthermore, we propose a novel application that greatly benefits from the method due to its nature: the generation of traffic scenes represented as graphs. Our method outperforms other graph generation methods, demonstrating a significant advantage in edge-related measures.

A key requirement for graph neural networks is that they must process a graph in a way that does not depend on how the graph is described. Traditionally this has been taken to mean that a graph network must be equivariant to node permutations. Here we show that instead of equivariance, the more general concept of naturality is sufficient for a graph network to be well-defined, opening up a larger class of graph networks. We define global and local natural graph networks, the latter of which are as scalable as conventional message passing graph neural networks while being more flexible. We give one practical instantiation of a natural network on graphs which uses an equivariant message network parameterization, yielding good performance on several benchmarks.

In the field of graphic design, automating the integration of design elements into a cohesive multi-layered artwork not only boosts productivity but also paves the way for the democratization of graphic design. One existing practice is Graphic Layout Generation (GLG), which aims to layout sequential design elements. It has been constrained by the necessity for a predefined correct sequence of layers, thus limiting creative potential and increasing user workload. In this paper, we present Hierarchical Layout Generation (HLG) as a more flexible and pragmatic setup, which creates graphic composition from unordered sets of design elements. To tackle the HLG task, we introduce Graphist, the first layout generation model based on large multimodal models. Graphist efficiently reframes the HLG as a sequence generation problem, utilizing RGB-A images as input, outputs a JSON draft protocol, indicating the coordinates, size, and order of each element. We develop new evaluation metrics for HLG. Graphist outperforms prior arts and establishes a strong baseline for this field. Project homepage: https://github.com/graphic-design-ai/graphist

Associating unstructured data with structured information is crucial for real-world tasks that require relevance search. However, existing graph learning benchmarks often overlook the rich semantic information associate with each node. To bridge such gap, we introduce the Multimodal Graph Benchmark (MM-GRAPH), the first comprehensive multi-modal graph benchmark that incorporates both textual and visual information. MM-GRAPH surpasses previous efforts, which have primarily focused on text-attributed graphs with various connectivity patterns. MM-GRAPH consists of five graph learning datasets of various scales that are appropriate for different learning tasks. Their multimodal node features, enabling a more comprehensive evaluation of graph learning algorithms in real-world scenarios. To facilitate research on multimodal graph learning, we further provide an extensive study on the performance of various graph neural networks in the presence of features from various modalities. MM-GRAPH aims to foster research on multimodal graph learning and drive the development of more advanced and robust graph learning algorithms. By providing a diverse set of datasets and benchmarks, MM-GRAPH enables researchers to evaluate and compare their models in realistic settings, ultimately leading to improved performance on real-world applications that rely on multimodal graph data.

Text-rich Graph Knowledge Bases (TG-KBs) have become increasingly crucial for answering queries by providing textual and structural knowledge. However, current retrieval methods often retrieve these two types of knowledge in isolation without considering their mutual reinforcement and some hybrid methods even bypass structural retrieval entirely after neighboring aggregation. To fill in this gap, we propose a Mixture of Structural-and-Textual Retrieval (MoR) to retrieve these two types of knowledge via a Planning-Reasoning-Organizing framework. In the Planning stage, MoR generates textual planning graphs delineating the logic for answering queries. Following planning graphs, in the Reasoning stage, MoR interweaves structural traversal and textual matching to obtain candidates from TG-KBs. In the Organizing stage, MoR further reranks fetched candidates based on their structural trajectory. Extensive experiments demonstrate the superiority of MoR in harmonizing structural and textual retrieval with insights, including uneven retrieving performance across different query logics and the benefits of integrating structural trajectories for candidate reranking. Our code is available at https://github.com/Yoega/MoR.

Recent prevailing works on graph machine learning typically follow a similar methodology that involves designing advanced variants of graph neural networks (GNNs) to maintain the superior performance of GNNs on different graphs. In this paper, we aim to streamline the GNN design process and leverage the advantages of Large Language Models (LLMs) to improve the performance of GNNs on downstream tasks. We formulate a new paradigm, coined "LLMs-as-Consultants," which integrates LLMs with GNNs in an interactive manner. A framework named LOGIN (LLM Consulted GNN training) is instantiated, empowering the interactive utilization of LLMs within the GNN training process. First, we attentively craft concise prompts for spotted nodes, carrying comprehensive semantic and topological information, and serving as input to LLMs. Second, we refine GNNs by devising a complementary coping mechanism that utilizes the responses from LLMs, depending on their correctness. We empirically evaluate the effectiveness of LOGIN on node classification tasks across both homophilic and heterophilic graphs. The results illustrate that even basic GNN architectures, when employed within the proposed LLMs-as-Consultants paradigm, can achieve comparable performance to advanced GNNs with intricate designs. Our codes are available at https://github.com/QiaoYRan/LOGIN.

Foundation models have emerged as critical components in a variety of artificial intelligence applications, and showcase significant success in natural language processing and several other domains. Meanwhile, the field of graph machine learning is witnessing a paradigm transition from shallow methods to more sophisticated deep learning approaches. The capabilities of foundation models to generalize and adapt motivate graph machine learning researchers to discuss the potential of developing a new graph learning paradigm. This paradigm envisions models that are pre-trained on extensive graph data and can be adapted for various graph tasks. Despite this burgeoning interest, there is a noticeable lack of clear definitions and systematic analyses pertaining to this new domain. To this end, this article introduces the concept of Graph Foundation Models (GFMs), and offers an exhaustive explanation of their key characteristics and underlying technologies. We proceed to classify the existing work related to GFMs into three distinct categories, based on their dependence on graph neural networks and large language models. In addition to providing a thorough review of the current state of GFMs, this article also outlooks potential avenues for future research in this rapidly evolving domain.

A legal knowledge graph constructed from court cases, judgments, laws and other legal documents can enable a number of applications like question answering, document similarity, and search. While the use of knowledge graphs for distant supervision in NLP tasks is well researched, using knowledge graphs for downstream graph tasks like node similarity presents challenges in selecting node types and their features. In this demo, we describe our solution for predicting similar nodes in a case graph derived from our legal knowledge graph.

Knowledge graphs have been proven extremely useful in powering diverse applications in semantic search and natural language understanding. In this paper, we present GraphGen4Code, a toolkit to build code knowledge graphs that can similarly power various applications such as program search, code understanding, bug detection, and code automation. GraphGen4Code uses generic techniques to capture code semantics with the key nodes in the graph representing classes, functions, and methods. Edges indicate function usage (e.g., how data flows through function calls, as derived from program analysis of real code), and documentation about functions (e.g., code documentation, usage documentation, or forum discussions such as StackOverflow). Our toolkit uses named graphs in RDF to model graphs per program, or can output graphs as JSON. We show the scalability of the toolkit by applying it to 1.3 million Python files drawn from GitHub, 2,300 Python modules, and 47 million forum posts. This results in an integrated code graph with over 2 billion triples. We make the toolkit to build such graphs as well as the sample extraction of the 2 billion triples graph publicly available to the community for use.

Graph representation learning has emerged as a powerful technique for addressing real-world problems. Various downstream graph learning tasks have benefited from its recent developments, such as node classification, similarity search, and graph classification. However, prior arts on graph representation learning focus on domain specific problems and train a dedicated model for each graph dataset, which is usually non-transferable to out-of-domain data. Inspired by the recent advances in pre-training from natural language processing and computer vision, we design Graph Contrastive Coding (GCC) -- a self-supervised graph neural network pre-training framework -- to capture the universal network topological properties across multiple networks. We design GCC's pre-training task as subgraph instance discrimination in and across networks and leverage contrastive learning to empower graph neural networks to learn the intrinsic and transferable structural representations. We conduct extensive experiments on three graph learning tasks and ten graph datasets. The results show that GCC pre-trained on a collection of diverse datasets can achieve competitive or better performance to its task-specific and trained-from-scratch counterparts. This suggests that the pre-training and fine-tuning paradigm presents great potential for graph representation learning.

Recently, an intriguing class of non-convex optimization problems has emerged in the context of learning directed acyclic graphs (DAGs). These problems involve minimizing a given loss or score function, subject to a non-convex continuous constraint that penalizes the presence of cycles in a graph. In this work, we delve into the optimization challenges associated with this class of non-convex programs. To address these challenges, we propose a bi-level algorithm that leverages the non-convex constraint in a novel way. The outer level of the algorithm optimizes over topological orders by iteratively swapping pairs of nodes within the topological order of a DAG. A key innovation of our approach is the development of an effective method for generating a set of candidate swapping pairs for each iteration. At the inner level, given a topological order, we utilize off-the-shelf solvers that can handle linear constraints. The key advantage of our proposed algorithm is that it is guaranteed to find a local minimum or a KKT point under weaker conditions compared to previous work and finds solutions with lower scores. Extensive experiments demonstrate that our method outperforms state-of-the-art approaches in terms of achieving a better score. Additionally, our method can also be used as a post-processing algorithm to significantly improve the score of other algorithms. Code implementing the proposed method is available at https://github.com/duntrain/topo.

Graph databases are gaining momentum thanks to the flexibility and expressiveness of their data models and query languages. A standardization activity driven by the ISO/IEC standardization body is also ongoing and has already conducted to the specification of the first versions of two standard graph query languages, namely SQL/PGQ and GQL, respectively in 2023 and 2024. Apart from the standards, there exists a panoply of concrete graph query languages provided by current graph database systems, each offering different query features. A common limitation of current graph query engines is the absence of an algebraic approach for evaluating path queries. To address this, we introduce an abstract algebra for evaluating path queries, allowing paths to be treated as first-class entities within the query processing pipeline. We demonstrate that our algebra can express a core fragment of path queries defined in GQL and SQL/PGQ, thereby serving as a formal framework for studying both standards and supporting their implementation in current graph database systems. We also show that evaluation trees for path algebra expressions can function as logical plans for evaluating path queries and enable the application of query optimization techniques. Our algebraic framework has the potential to act as a lingua franca for path query evaluation, enabling different implementations to be expressed and compared.

There are few known exponential speedups for quantum algorithms and these tend to fall into even fewer families. One speedup that has mostly resisted generalization is the use of quantum walks to traverse the welded-tree graph, due to Childs, Cleve, Deotto, Farhi, Gutmann, and Spielman. We show how to generalize this to a large class of hierarchical graphs in which the vertices are grouped into "supervertices" which are arranged according to a d-dimensional lattice. Supervertices can have different sizes, and edges between supervertices correspond to random connections between their constituent vertices. The hitting times of quantum walks on these graphs are related to the localization properties of zero modes in certain disordered tight binding Hamiltonians. The speedups range from superpolynomial to exponential, depending on the underlying dimension and the random graph model. We also provide concrete realizations of these hierarchical graphs, and introduce a general method for constructing graphs with efficient quantum traversal times using graph sparsification.

We investigate novel random graph embeddings that can be computed in expected polynomial time and that are able to distinguish all non-isomorphic graphs in expectation. Previous graph embeddings have limited expressiveness and either cannot distinguish all graphs or cannot be computed efficiently for every graph. To be able to approximate arbitrary functions on graphs, we are interested in efficient alternatives that become arbitrarily expressive with increasing resources. Our approach is based on Lov\'asz' characterisation of graph isomorphism through an infinite dimensional vector of homomorphism counts. Our empirical evaluation shows competitive results on several benchmark graph learning tasks.

Large Generative Models (LGMs) such as GPT, Stable Diffusion, Sora, and Suno are trained on a huge amount of language corpus, images, videos, and audio that are extremely diverse from numerous domains. This training paradigm over diverse well-curated data lies at the heart of generating creative and sensible content. However, all previous graph generative models (e.g., GraphRNN, MDVAE, MoFlow, GDSS, and DiGress) have been trained only on one dataset each time, which cannot replicate the revolutionary success achieved by LGMs in other fields. To remedy this crucial gap, we propose a new class of graph generative model called Large Graph Generative Model (LGGM) that is trained on a large corpus of graphs (over 5000 graphs) from 13 different domains. We empirically demonstrate that the pre-trained LGGM has superior zero-shot generative capability to existing graph generative models. Furthermore, our pre-trained LGGM can be easily fine-tuned with graphs from target domains and demonstrate even better performance than those directly trained from scratch, behaving as a solid starting point for real-world customization. Inspired by Stable Diffusion, we further equip LGGM with the capability to generate graphs given text prompts (Text-to-Graph), such as the description of the network name and domain (i.e., "The power-1138-bus graph represents a network of buses in a power distribution system."), and network statistics (i.e., "The graph has a low average degree, suitable for modeling social media interactions."). This Text-to-Graph capability integrates the extensive world knowledge in the underlying language model, offering users fine-grained control of the generated graphs. We release the code, the model checkpoint, and the datasets at https://lggm-lg.github.io/.

Recently, graph neural networks (GNNs) have shown prominent performance in semi-supervised node classification by leveraging knowledge from the graph database. However, most existing GNNs follow the homophily assumption, where connected nodes are more likely to exhibit similar feature distributions and the same labels, and such an assumption has proven to be vulnerable in a growing number of practical applications. As a supplement, heterophily reflects dissimilarity in connected nodes, which has gained significant attention in graph learning. To this end, data engineers aim to develop a powerful GNN model that can ensure performance under both homophily and heterophily. Despite numerous attempts, most existing GNNs struggle to achieve optimal node representations due to the constraints of undirected graphs. The neglect of directed edges results in sub-optimal graph representations, thereby hindering the capacity of GNNs. To address this issue, we introduce AMUD, which quantifies the relationship between node profiles and topology from a statistical perspective, offering valuable insights for Adaptively Modeling the natural directed graphs as the Undirected or Directed graph to maximize the benefits from subsequent graph learning. Furthermore, we propose Adaptive Directed Pattern Aggregation (ADPA) as a new directed graph learning paradigm for AMUD. Empirical studies have demonstrated that AMUD guides efficient graph learning. Meanwhile, extensive experiments on 14 benchmark datasets substantiate the impressive performance of ADPA, outperforming baselines by significant margins of 3.96\%.

Large language models are extensively applied across a wide range of tasks, such as customer support, content creation, educational tutoring, and providing financial guidance. However, a well-known drawback is their predisposition to generate hallucinations. This damages the trustworthiness of the information these models provide, impacting decision-making and user confidence. We propose a method to detect hallucinations by looking at the structure of the latent space and finding associations within hallucinated and non-hallucinated generations. We create a graph structure that connects generations that lie closely in the embedding space. Moreover, we employ a Graph Attention Network which utilizes message passing to aggregate information from neighboring nodes and assigns varying degrees of importance to each neighbor based on their relevance. Our findings show that 1) there exists a structure in the latent space that differentiates between hallucinated and non-hallucinated generations, 2) Graph Attention Networks can learn this structure and generalize it to unseen generations, and 3) the robustness of our method is enhanced when incorporating contrastive learning. When evaluated against evidence-based benchmarks, our model performs similarly without access to search-based methods.

Subgraph matching is a fundamental building block for graph-based applications and is challenging due to its high-order combinatorial nature. Existing studies usually tackle it by combinatorial optimization or learning-based methods. However, they suffer from exponential computational costs or searching the matching without theoretical guarantees. In this paper, we develop D2Match by leveraging the efficiency of Deep learning and Degeneracy for subgraph matching. More specifically, we first prove that subgraph matching can degenerate to subtree matching, and subsequently is equivalent to finding a perfect matching on a bipartite graph. We can then yield an implementation of linear time complexity by the built-in tree-structured aggregation mechanism on graph neural networks. Moreover, circle structures and node attributes can be easily incorporated in D2Match to boost the matching performance. Finally, we conduct extensive experiments to show the superior performance of our D2Match and confirm that our D2Match indeed exploits the subtrees and differs from existing GNNs-based subgraph matching methods that depend on memorizing the data distribution divergence

Retrieval-augmented generation (RAG) is a powerful technique that enhances downstream task execution by retrieving additional information, such as knowledge, skills, and tools from external sources. Graph, by its intrinsic "nodes connected by edges" nature, encodes massive heterogeneous and relational information, making it a golden resource for RAG in tremendous real-world applications. As a result, we have recently witnessed increasing attention on equipping RAG with Graph, i.e., GraphRAG. However, unlike conventional RAG, where the retriever, generator, and external data sources can be uniformly designed in the neural-embedding space, the uniqueness of graph-structured data, such as diverse-formatted and domain-specific relational knowledge, poses unique and significant challenges when designing GraphRAG for different domains. Given the broad applicability, the associated design challenges, and the recent surge in GraphRAG, a systematic and up-to-date survey of its key concepts and techniques is urgently desired. Following this motivation, we present a comprehensive and up-to-date survey on GraphRAG. Our survey first proposes a holistic GraphRAG framework by defining its key components, including query processor, retriever, organizer, generator, and data source. Furthermore, recognizing that graphs in different domains exhibit distinct relational patterns and require dedicated designs, we review GraphRAG techniques uniquely tailored to each domain. Finally, we discuss research challenges and brainstorm directions to inspire cross-disciplinary opportunities. Our survey repository is publicly maintained at https://github.com/Graph-RAG/GraphRAG/.

Graph Neural Networks (GNNs) have already been widely applied in various graph mining tasks. However, they suffer from the shallow architecture issue, which is the key impediment that hinders the model performance improvement. Although several relevant approaches have been proposed, none of the existing studies provides an in-depth understanding of the root causes of performance degradation in deep GNNs. In this paper, we conduct the first systematic experimental evaluation to present the fundamental limitations of shallow architectures. Based on the experimental results, we answer the following two essential questions: (1) what actually leads to the compromised performance of deep GNNs; (2) when we need and how to build deep GNNs. The answers to the above questions provide empirical insights and guidelines for researchers to design deep and well-performed GNNs. To show the effectiveness of our proposed guidelines, we present Deep Graph Multi-Layer Perceptron (DGMLP), a powerful approach (a paradigm in its own right) that helps guide deep GNN designs. Experimental results demonstrate three advantages of DGMLP: 1) high accuracy -- it achieves state-of-the-art node classification performance on various datasets; 2) high flexibility -- it can flexibly choose different propagation and transformation depths according to graph size and sparsity; 3) high scalability and efficiency -- it supports fast training on large-scale graphs. Our code is available in https://github.com/zwt233/DGMLP.